Yes, they most definitely CAN spot the bubble wake left by the torpedos (case in point, the torpedo tutorial - if you fire first at the stationary merchant, he hauls ass like crazy to get out of the way).
3 things you can do to help lessen their chances of noticing them until it's far too late:
1. Avoid daytime attacks or anytime visibilty is good. Overcast evenings with slightly choppy seas are best.
2. Try to get as close as possible to give them less reaction time if they do happen to spot one of your eels.
3. your electric torps have a higher malfunction rate but on the plus side you won't have to worry about them leaving a telltale wake; this is useful for daytime attacks/convoy attacks...etc
Hope this helps.
