I find this confusing. They're completely optional and excludable. Why deny them to those groups who find them useful?
You can use them as little or as much as you want to. As the DM, you make that call. Including them allows people who would make a different choice to you the option; omitting them gives those people no option.
I can't get behind the concept of excluding options because 100% of the customers won't use them. Better to include them and let people choose to not use them.
In WotBS some of them are closely tied to the plot in ways that may not be obvious until 2-3 modules later. A DM who has eliminated Torrent in module 1 without reading Shelter from the Storm (#3), may not realize how important it is that one of the PCs have a connection with Lee Sidoneth, and probably the Lyceum as well. Missing this makes it harder to run Shelter as written.
Haddin reoccurred near Vidor at the beginning of module 5 after I had killed him off previously. Surprise! Most of my reading ahead in the series has been from the 3.5 version that I bought originally, and this was an added plot thread in 4E, so I had no idea it existed. I used Paradim instead, since he escaped the fight at the end of Shelter (actually his fate is never mentioned) and my characters despise loose ends and escaped villains. Also that stuff with trolls in Vidor wound up being resolved as they traveled through on the way to Bresk, rather than on the way back as written. There is no way my group would ever hear about a village in immediate danger and ignore the problem until weeks later when they got back from their diplomatic mission.
Of course they investigated immediately, and so found biomanced trolls and Paradim, who despite being about 4 levels higher and having lots of nasty trolls with him, they killed just before he could escape alive. It's okay though, his remains teleported away as they killed him. My group may think I was trying to deprive them of treasure, but it's actually because he had already crafted a phylactery and bound his soul to it. He'll be back.
Katrina is pretty thoroughly woven into the story, but you don't have to drag her along for three modules before dropping her off in Seaquen. The problem there is actually getting the party to talk to her enough to influence her course of action in later modules. They rescued her, they see she found a job as Simeon's secretary, she is no longer their concern. That's where I am at right now.
In any case, various NPCs are woven into the story in ways that the DM may not have anticipated because he hasn't read ahead 3 or more modules from the current adventure. What you could do is include a sidebar for each NPC with information on what to do if the NPC doesn't go with the party or is eliminated entirely.
i.e. What if Torrent Doesn't Go With Them?
Torrent's relationship with her mentor Lee Sidoneth and background as a student of the Lyceum Academy wil be important in future adventures. If you choose to remove Torrent from the story, or have her stay in Gate Pass rather than traveling with the party, then it is important that one or more of the PCs have this connection instead. Any arcane caster could be a student of the academy, or perhaps one of the characters grew up in Seaquen and knew Lee from his time there.
The problem with eliminating any NPC now is that I don't always know when that character will come back as a plot element in the future. It hasn't stopped me from doing it, but I always feel I need to read ahead a lot so I can find out the consequences before making a change. For instance Tiljann never went with them so all the stuff with Etinifi is really never going to come up until they find him. They won't know who he is or particularly care that they have found him. Just another crazy prisoner. I will need to rewrite a lot of that. So a decision I made in module 2 is creating an issue in module 8.
Make it clear to the DM which NPCs are strictly optional, and the changes you need to make if you remove them, and that solves the problem. Stat them out as companion characters to make them easier to run and you're golden.