The more you keep your TC at 32 or less the quicker your crew will tire.
In theory, if you could play the game continually at TC > 32, your crew would never tire. Of course, that can't happen.
So yes, low TC trips through the canal will affect your crew. Make sure they are all (well, as many as possible) in the rest compartments. There's no point having your torpedo compartment manned, for example, when entering or leaving the canal.
And as P_Funk suggested, raise your LandProximity TC value to something like 128 (min - I run at 512 and have never had an "accident"). Search the forum for instructions on how to do so - it's commonly asked.