The A.I pirates keep doing this.Not a wise strategy.

Another major issue is the A.I are building lots of scout cruisers for warships.

Are those the pirates that are attacking with transports or was it Marauders

Never saw such a pirate attack with transprots yet (though they do sometimes have transports in their systems for lore reasons)
In case of Marauders, it is simply the way they bring their slavers into the system and for attack. They also use these transports to bring back the captured slaves to their base

Regarding Scout ships, only propep empires should produce scouts and though it sometimes happens that they overdo this a bit I wouldn't worry abouth that much. On large maps, they simply roll out many of these and later these get crammed together when there is not much left they can explore but it does not cause a signifficant burden for the AIs budget, and they are not produced anymore from mid-game