A lot of players love getting attached to random NPCs, all of your Boblin the Goblins. Some games encourage that friend recruiting loop. However, once you get over a certain number of allies, they turn from potentially interesting people into faces in the crowd. It might be good to prepare for that ahead of time.
Our group has played a lot of games across a lot of systems. Like many groups, we tend to hoard NPCs and add anyone with a name to our "friends pile". In our biggest game, Princes of the Universe, we had like 50 named important NPC alliess that were on PC's level (on top of a number of lesser named mooks). Unfortunately, as we realised, that number is too big for players to handle, and 95% of them pretty much remained as background characters nobody cared about as the same 3-4 NPCs were always at the forefront.
More recently, we started playing a lot of Fellowship. It's a flexible fantasy game where you can solve your problems in many ways, Undertale or Steven Universe hugs included. The system also encourages you to recruit a lot of a lot of NPCs since you can use them as boosts in future conflicts. At the same time the game expects you to keep track of those NPCs, their health and stats, as wel as how many friendship levels you have with them and what statements are tied to them. It can become a lot to keep track of when you can easily recruit a few Boblins each session.
It's probably better to accept that most NPCs the players recruit won't be too important and anticipate that both from GM prep perspective, as well as game design perspective. If some NPC turns out to be more impactful, they can be fleshed out more between sessions and upgraded to a more prominent status.
From a game design perspective, you could have important NPCs with full stats and relationships, and minor NPCs that go together on a roster you can "spend" them from to get some appropriate bonus some limited number of times before they move on or fade from importance. Sure, nothing is stopping you from forming a small army of those NPCs, but that would probably fall under different rules than individual companions.
Even your roster of core NPCs will probably be small. From our experience players usually tend to care about one or two key NPCs at a time, and then having a few more in well-defined roles ("these are my two pet wargs", "here are my parents that I begrudgingly interact with as a teen") but are rarely important to draw too much attention to.
Of course this doesn't have to be a hard rule, I'm mostly sharing the observations we had while playing our games.
Conclusions
Players tend to recruit a lot of NPC allies, but often those allies tend not to contribute much to the party or the game afterwards. It's good to be able to place NPCs on an importance scale and handle them accordinly. Players will usually only focus on one or two NPC friends, while others will just become background. It's good for games to also be able to distinguish between important NPCs and the less important ones and don't treat both of them with the same granularity.
