I'd like to see these vessels added to Enigma for several reasons:
1. Just to fill the vast empty sea.
2. Such vessels can report your position to the enemy, so they can be valid targets. However, sinking them will deplete your torpedo stores during crucial missions, so that may become a critical decision. (An excellent hurdle)
3. Such vessels need not be what they seem. Liners could be armed like Q-Ships, and fishing boats could packed with explosives, just hoping to get close.
4. Tugs, specifically, are very valid targets as they will assist enemy vessels into dock.
5. Human Shields / Running Interference. Such vessels, like tugs and trawlers might be used to escort vessels, and while they are probably crewed by the enemy, sometimes the objective is too important to avoid destroying them.
6. While honorable commanders should only pursue military targets, their orders may be to wage a war of terror on the enemy, and that would mean everything is fair game.
While many of those reasons are good enough to add them, I think pure realsim is probably the most important one.
An example...
Entering New York City Bay in my sub at night, passing the Statue Of Liberty and Ellis Island, waiting for the Staten Island Ferry to pass by, and firing a few torpedoes into the Brooklyn navy yard.
If the ferry gets in the way...so be it.