Well if he goes after the transports he gets some as the others presumably scatter but that requires 20/20 hindsight. At the time Mikawa has very limited knowledge of what is going on or US intentions and has just won a signal victory. The US forces have been ashore for 24 hours which is plenty of time to have unloaded everything valuable. So he sinks some transports.
The risk if there are carriers ( and unless the USN has provided no air cover at all there will have been yesterday) nearby is his CA will get caught in daylight for sinking some transports that may or may not be loaded.
On my understanding, though, his fear of American carriers was probably secondary in the decision. The time needed to reload tortpedo tubes after the battle worried him (he was low on shells, too), requiring such time that they'd have to stick around through daylight.
But the whole point of the op was to go in and get those transports. Which he now had the chance to do. Had he proceded immediately, without torpedoes, he would be taking a calculated risk that there were no more surface combatants of note in the Slot, and that you won't get dunked on in daylight on the way out. But I think this is the kind of risk that Japanese commanders have to take at this point. And after all, you just blew up a whole squadron of Allied heavy crusiers - what else do you really think is going to be standing in your way?