Bottom line is it depends on your software and the settings you use. If you've got subs of differing lengths then you need master darks and master bias frames so the program (if it can) can calculate a "virtual master dark" for each exposure length.
The other problem is the longer subs will generally show lots more detail, so for faint fuzzies you're have to decide if there'll be any dilution in signal by including the shorter subs just to try and reduce noise. I'd suggest it will depend a lot on objects, variation in times, light pollution among other things.
(was that wishy washy enough!?...
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