I'm almost certain ships react - yesterday, I had one case where as soon as I fired a torpedo, the ship sped up, causing me to miss, and another case where they slowed down.
Unfortunately, other ships in the convoy don't seem to react then when you hit one - yesterday, everybody in the huge 10-12 ship convoy just sort of kept plodding along while I picked them off one after the other.
I know there's a mod for better escorts, I wish there was a mod for smarter merchant AI - reacting even better to torpedo wakes but especially to explosions.