Here's the most hackerly way to do this: rent a 10MHz, 10-bit or better data acquisition rig and hook its probe to the head amplifier of your VTR. Play all your tapes and capture the raw tape signal to your computer. This will only require 45 GB per hour, i.e. almost nothing. Process the signal after the fact, with perfect field/line sync correction, whatever audio compression/limiting/equalization you want, etc.
VHS only has 3MHz bandwidth, let's don't pretend that a software-defined VTR is not practical.
Answering your actual question: S-VHS vs VHS deck should not make any difference for playback of VHS cassettes. Cassettes recorded in S-VHS cannot be played on a VHS deck, so that would be an obvious difference.
There are in fact proof-of-concepts similar to what you describe[1] (this one is based off the Doomsday Duplicator[2], a hardware device used for Direct RF capturing off laserdisc players).
My (admittedly basic) understanding of VHS vs S-VHS decks is that due to the stricter tolerances required by the S-VHS standard, S-VHS decks typically have better transports than regular VHS decks (lower wow/flutter, better tracking, etc...). And of course many of the high-end decks have a built in TBC.
Nice. It really warms the ol' cockles to see that level of dedication to preservation. There already has been for years NTSC decoding in the gnuradio project, so doing this to VHS if you happen to have a USRP or similar peripheral might be almost trivial.
Wow, this is taking me back to a former life of mine! The idea of a built-in TBC scares me a bit though. I guess it's not a big deal if you don't plan on mixing with other sources. I'd always prefer the shared black-burst generator in that case.
VHS only has 3MHz bandwidth, let's don't pretend that a software-defined VTR is not practical.
Answering your actual question: S-VHS vs VHS deck should not make any difference for playback of VHS cassettes. Cassettes recorded in S-VHS cannot be played on a VHS deck, so that would be an obvious difference.