You can activate the ally abilities on any card where you have played another card of that faction - there is no limit to the number of ally abilities you can activate and one card can active multiple other cards.
can i decide now (after that I played Supply Bot) to use Cutter ally ability and Federation Shuttle ally ability (and so do not use Defense Center ally ability) ?
You can use the ally abilities on all 3 (but you don't need to use any if you don't want to), but with those 3 then you may as well.
can i decide now (after that I played Supply Bot) to use Cutter ally ability and Freighter ally ability (and do not use Federation Shuttle ally ability) ?
Again you can use the ally abilities on all 3 ships whenever you want during your turn. You can buy a cheap card (hoping for a better ship to top deck) then activate the Freighter ally ability and buy the ship you just revealed.