The squad numbers never get full up because I reasign them every season and only the 30 or so players who I think will be regular contributors are given a number, along with any Fred that has appeared in the senior team, (I work from 99 downwards on Freds).
Also, as soon as a player goes out on loan he allocated number is taken away from him.
99 players sounds a lot, but consider this.
15(ish) players in the youth team.
20(ish) players out on loan at any 1 time.
10(ish) players injured at any 1 time.
14 players required to play in Reserve league games.
30(ish) senior players who will alternate between senior league & cup games.
That takes us to 89 players and leaves 10 to form the nucleus of a squad that is I suppose half-way between the Reserve League team and the senior team. These players play in the 2nd tier of Cup games and fill in in the senior squad on occasion, as well as fleshing out the Reserve squad.