From experience in the early days of daw's I will say that there most certainly was a difference between logic, cubase, pro-tools and motu.. easy to hear.
as the programs evolve and computers beome faster the differences become more slight as one would expect, and it's harder to hear the differences. Which doesn't mean there aren't any sonic differences.
but an older program on a slower computer running at 16/44.1 sounds worse than a new program at 16/44.1 on a newer computer...Just had a friend switch from logic 4.8 to cubase sx for example.
this only proves that, although both systems should be ideally reproducing the waveform perfectly, in fact there are technical issues which influence the sound quality that go beyond mix engine bits, sample/bit rate etc.
there is also the fact that computer code is inaccessible, and too complex for us end-users to disassemble and study or modify.. so only direct experience with the product will be of any value: love it or leave it.
perfection does not exist, regardless of what people say about digital... it's been perfect from day one as far as the people who earn money from it are concerned.
on the up-side, if you choose a DAW as your primary recorder and mixer then you are probably much more concerned with edit-ability and recall than such fine distinctions in audio quality so the differences are probably not worth noting too much.
I wonder if anyone has found what daw works best for classical music or acoustic music.