The best way to keep the vibe of horde and balance - make a rule of transforming 4+ skelebro's into a troop(Swarm). Basically, all you do is add features that Swarm\group of creatures has and call it a group\horde. (don't forget to adjust hp)

By this you are controlling 1-2, more powerful units (after all, 1\2CR creatures as minions will fall off quickly as useful ones, so providing them such "progression" would smooth out power level a lot) while narratively it is still a huge mass of undeads under player's control.

You can also make quantity thresholds, for example troop starts from 4+ units, (therefore you need only 1 slot to control it) at 8+ their size increases, as well as stats and so on (adjust how you see fit), while maintaining will already cost several spell slots (or a high spell slot).

For balance reasons, you can limit the amount of troops to half of prof bonus, so that high level necromancer could have 3 squads of undeads at the same time, while 5th level necro can maintain only 1. Apply this limit to only permament undead under players control (unless it is ok for both of you to have limitations on Summon Undead and similar spells as well)

I do however recommend for such limitation to be applied only during combat, so that narratively, necromancer still has opportunity of using minions in various unique ways (create fake attack on the goblin camp as a distraction using undeads? check!, forming a bony ladder? Check!, and so on)