Not that anyone has run into. My own Mythology mod adds hundreds of buildings and hundreds of unit types, and I haven't seen any issues. Likewise, my Ascension mod adds 45 techs, with even more buildings and units. So far, no obvious problems other than the promotion issue. Other big content mods have added even more buildings/techs/units, again with no issues.
You'll know when you're over the promotion cap; if you've got 201 promotions, then every unit in the game (even the starting Warrior and Settler) will get the 201st promotion for free. If you've got 205, then they'll get the last five for free. And so on. Very easy to keep track of this way.
We've been told almost nothing on the modding side about the expansion. I would guess that the expansion will add a number of new promotions to the game; if they DON'T find a way to remove the cap, then we'll be in real trouble. But they might just increase the cap to 250 or something, to allow for 50 new promotions in the expansion, in which case we'll be no better off than we are currently. (While it's possible that the current cap is not something they explicitly set, it's just really hard to believe that a cap of exactly 200, a nice round number, WASN'T something they added themselves.)