Yes, the 5e adventures do seem to incorporate a lot of potential NPC allies, don't they? It's possible to collect lots of NPC hangers-on in Curse of Strahd as well. I think it's one of the ways they justify throwing lower level heroes at higher level threats (eg. giving the PCs some storm giants to make fighting a mighty blue dragon at 10th level more fair).
Even the 1st Edition modules provided NPCs (I'm thinking Temple of Elemental Evil), but usually staged them in. The Gold-box games always provided 2 NPCs for a party of 6 as well.
I like the rules given in ToA that conform to the Dungeon Master's Guide on Loyalty. If you have someone in the party with a Charisma of 20 (should be impossible until at least Level 4), then NPCs should join the party into the dungeon, ruins, shrine, monastery, mine, or other mapped encounter. Some NPCs like Hew are compelled to enter Wyrmheart Mine, Musharib to Hrakhamar, Eku to Mbala, Faroul/Gondolo to Needle's Bones, and Azaka to Firefinger. If, during the course of any dungeon delve, a party member saves the life or gives the key magic item to the NPC -- then the NPC's Loyalty will rise to an acceptable rating where the NPC may join for another dungeon delve -- but only then.
If the party struggles with a mapped encounter, say that they lose a key party member or a key item is visibly lost, then when they return to camp the NPCs should drop their Loyalty ratings. Death of an NPC may cause a significant drop in Loyalty of all other NPCs. Statuses such as frightened, poisoned, diseased, or high spell/magic damage will also impact Loyalty. NPCs given magic items once to raise above a Loyalty of 10 might expect a new magic item during each and every dungeon delve, resulting in further Loyalty rating losses (and increasing over time due to increasing expectations -- often becoming unreasonable).
Curse of Strahd can definitely benefit from these rules as well, but Curse of Strahd gives a few more-easy outs for the NPCs. Some of the key NPCs will extra-dimension travel, or they will stay stuck in their ways (refusing to leave their current highly-protected area, such as their hometown). I think Tomb of Annihilation will need similar outs. Sometimes, an NPC will take their ball and go home, so to speak. They will cut their wins and they will cut their losses -- often at exactly the wrong time for the party. The party will have to learn to make do.
I am much-less worried about the early-on sidequesters such as Undril Silvertusk (half-orc priest), Inete the acolyte, and Eshek (another acolyte) -- especially if they are only with Eku (again, she had a strength/dexterity of 10 and a quarterstaff as far as the party knows) and Qawasha/Kupalue. These are the perfect campers and scouts. They can get themselves into a small amount of trouble here and there with the party to rescue them with minimal reciprocation other than casting rituals or full-party heals.
Random encounters with other explorers, the Emerald Enclave, and perhaps even the Flaming Fist can create scenarios for an NPC (or a few) to take their leave from the party. The well-meaning humanoids just happen to be heading back to Port Nyanzaru or Fort Beluarian -- and the NPC is ready for a change, especially after a big battle.
Later-game NPCs such as Artus and Dragonbait should be easier to balance while still keeping them around. They'll know when to long rest twice on their own -- they make their own decisions. They are their own party, but it just-so happens that their goals align with the party more-often than not.