In Chapter 93 (part 3 of "Class Reunion") of the manga, Bartender, a customer who walks into Eden Hall informs Sasakura that he doesn't have a reservation. IIRC, I've seen this happen before too. Is it common for Japanese bars to require advance reservations? While I can understand booking tables, Eden Hall only appears to provide barstools.
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Japan is a crowded place, specially downtown Tokyo. Often, people meet after work with several others somewhere. If 5+ people want to meet in a bar and come late, and want to make sure that person 1-4 can sit down while they are waiting for person 5, you better book. Other bars simply do not want people standing around since they think this gives the bar a lower image. If you cannot sit, you cannot come in.
Then, on top of that, there are bars (and restaurants) that simply do not allow walk-in guests. You will have to be introduced by a already known person to the bar in order to be able to get in. They will tell you that you cannot come in without a reservation, but you will also not be able to make one, specially not on busy days.
So the upscale bars where most of the room is filled with the bar (if they have one), heavy upholstered bar stools and tables/chair arrangements (imagine a bar in a fine hotel with lounge-like environment, see image below) will not allow you to stand. If you do not have a space for you to sit down, they will excuse politely and this is your cue to leave.
The best way of dealing with this is simply calling each time you go somewhere without having been there before. Unless you are dealing with a chain store (like the "Hub" Irish bar chain in Tokyo or others), it will be difficult to know from the name what to expect. One hint can always be their website. Even if you do not understand Japanese on the website, if they have photos where you see a major part of the bar without chairs so people can stand around, you can assume that you do not need to reserve.
If you however have a special bar in mind to go, and want to make sure that you will have a space there for you and your friends (one person can often be seated, 5 is tricky in most places), you better call and check.