That's a good point I feel, if they are temp. Personally I never used that ability I admit. Is it worth it. I typically just turn them into pure heal bots but I suppose if you got like 10 of them later in game it can be pretty nutty.
It's good if you are trying to swarm say a starbase or it can provide a quick fleet boost for a large battle. Usually by the time you get the ability though, your fleet should already be pretty huge so the extra ships are just icing on the cake at that point. Still a fun ability, but some of the fun is removed when you lose real ships but can't replace them until the replicated ships expire due to them taking up fleet supply.