Of course are there differences. At lvl 120 you need less vets /experts to reload cap them. But that would be senseless in my eyes.
If you calss at Yamato level (89) and use them with a normal amount of vets (109) and experts you will reach the reload cap somewhere in level 110-115 probably. Using those AA gunners will gain you some extra experts in addition.
Personally I don't see a reason to NOT class them at level 90. Yamato and SY have better AA setup than Amagi so you will definatly like to use them there.
Only point is: If you haven't played AA battleships until now be careful with it. I see lots of BB players AAing around not recognizing that they ran into enemy range meanwhile - and BOOM they are dead. If you hang back for AAing you should now that the front line is where your BB4/5 belong - so you will weaken your team too. In my opinion IJN and MN AA is nice for scout sniping and is very usefull in BB only battlerooms which are no longer played. I've only seen a few good BB players handling AA and main weapons well in GB rooms.
Personally concerning GB, HA and fleetwar rooms I consider a non AA setup with 2 additional reps more useful nowadays (you won't have time to AA in fleetwar rooms when linefighting with enemy fighters above your ship). But you won't choose IJN with such a setup either.