I will start by some disclaimers, I will make references to my personal experience in March-April 2023, so do not expect to see and find exactly the same things, but this should still be a good baseline for your own travel. Second disclaimer, in order I am mostly fan of Nene, Pekora and Miko and mostly purchased their merch.
The first thing you will want to do is to closely monitor Collabo cafe and PR Times before and during your trip, those will be your major source of information an upcoming events and new products. Also be aware that most goods are offered for a limited time, stores do not stock old merchandise, so you might be more or less lucky depending on what is released during your trip and what kind of item you are looking for. Also try to be aware of the market cost of the items you want to buy, maybe shop around, especially if you are in a big city.
During my first days, Sakura Miko had a collaboration with the taiyaki store chain Naruto Taiyaki Honpo. The theme was on point as Miko like taiyaki and the special menu item was sakuramochi flavored. It was, good, but sakuramochi is not my favorite flavor to start with. The theme ambiance was minimal with only a cardboard cutout of Miko. The small plushies were already sold out in two stores and I decided to get an acrylic stand, even if it is not my favorite piece of merch. I also got a postcard with my purchase.
I was also able to visit Raku Spa in Miyazaki on the last day of the collab with 4th gen. I decided to go to he restaurant only and not do the spa, so you don’t have to go if you only want to try the food. As the event take place in a spa, most of the customers are not there for the collab. This means that the themed ambience is at a minimum, there was banners and cutout of the four members in a small room, so it was still nice to see. It also means you do not need a reservation. I decided to get the nna-tantan-men, that I thought was good. The theme on the food preparation is minimal, you only get a small image of the member with the dish. However, at least for Luna, the food selection was clever as she is known to like takoyaki and the pun with her nickname, Luna-tan, and the tantan-men is kind of fun. In general, I would agree with the common impression that collab cafe are overpriced. Looking at their regular food and drink menu, I would say that the collab items are probably around 500¥ more expensive than a regular item on the menu, all that for a random coast (or two) for each item ordered. I only took one dish and ended up with a Luna coaster. I also got a postcard for following Raku Spa on Twitter and retweeting their post. I am glad that I got all Luna items as she is my favorite of the four, but I did not go as far as to buy other piece of merch.
Overall, I was happy to get those two experiences. I would probably go to other events like the first one or something like the collab with Bakudanyaki that happened under Pekora influence, as long as the items are roughly he same price as regular price. As for the collab cafe, I would probably skip it unless it features one of my favorite member. Also note that while some collaborations do happen nationwide, there is also many that are limited to a single location and in that case it is usually around Tokyo.
As there is different types of merchandise, where to find them will depend on the type of item.
I found food items, the cracker and wafer with a card or sticker, in many different kind of stores including convenience store, grocery store, Donki, Book Off Super Bazaar and different anime stores. Do not expect to find it everywhere, if you keep an eye open, you can find it in stores you would not expect.
For sake, the only place I saw the Pekora umeshu and Noel gin was at the gift shop on the first floor of Radio Kaikan in Akihabara.
Books, CD/BluRay, such as HoloX Meeting manga or Marine & Noel illustration book, etc, or any of the music or show release, manga stores in general would be a good start and Animate seems to be a valid option anywhere in Japan.
Game cards, new pack seems to be hard to get unless you pre-order them in a store and possibly online. You can still find individual cards for 30¥ to 100 000+¥ by cards, depending on the rarity, in second hand stores.
General merch, I found some Hololive items in almost every Animate I visited across Japan, but the selection was really different from one place to the other. While I could find some remaining items from the Pekora collab from January in Tokyo, in other places I started to see Hololive Error cards and sometimes wafers. Other anime/manga also have items.
Of course, any collab items would be found in the specific store, for example the upcoming Shiraken x Animate items will be found in Animate or 3rd gen x GiGo at GIGO arcade and the convenience stores items will be in the specific chain, just check if there is a list of participating stores as the Family Mart items were not in all stores, and not even easy to spot when they had it (as opposed as Kamen Rider that took a lot of place).
Figures, the relax time series is present in arcades all over the place, they often have different figures available, but you might have to look in several arcades for a specific one, you might also find them at second hand shops if you are not into crane games. Other figures can be found in stores that sell figures, I would often see some of them in many stores all around Akihabara.
Also check capsule toy from Bandai Namco as they ran several series of keychain.
Doujin, here it can get wild. I had good luck at MelonBooks, where there was a good Hololive section. I personally decided to buy some by Nishizawa 5mm, as she is the illustrator for Nene. You might have some luck in other stores that sell doujin.
Finally, the big secret is second hand stores. While in Akihabara, Radio Kaikan and Akiba Culture Zone have several stores that sell second hand items. You can find anything here, tapestry, acrylic stand, badge, cards, keychain, clear file, almost anything. You can even find official birthday/anniversary merch, including the complete set signed cards. Here the secret is to go to as many stores as you can as they will offer different things. You will likely find things in Lashinbang all around Japan.
Overall, I found that it was not too difficult to find Hololive items, even in some unexpected places, like in Kanda-myojin. But at the same time, they are not as present as other franchises such as Demon Slayer, Spy x Family and Uma Musume that are really everywhere right now. The main thing is to keep an eye open as you never know what you can find. It might also good to set yourself some budget limit or goal of items to buy because the temptation can be strong. Also don’t forget to check if stores offer tax free if you purchase for more than 5500¥ in a single store.