Stretch modes are entirely dependant on the blitter being used, and if that blitter can offload to the video card.
Using something like DirectDraw, when doing stretching of an image you can easily offload the stretch function to the video card if you use something modern like a GeForce or Radeon card, and the proper drivers. That's also the reason why you cannot turn off the bilinear filter on DD stretching with these cards, because it's done at a card level and not at a software level.
Likewise if you are using SVGA or VBE, some cards can happily stretch images using video hardware with the correct VESA extensions in hardware.
If however you're using a particular blitter to do the stretch, and either you have the wrong drivers (or none at all loaded) or a card that doesn't support the particular type of stretch then the stretch will be done by the CPU, and in turn interfere with performance.
The best way to test this is empirically using the benchmarking features built into MAME. On my main workstation (GeForce4 video card, using SDL under Linux), rendering at 1024x768 compared to 640x480 makes negligable difference (1 or 2 frames per second in games running at 300FPS anyway). Likewise on my MAME cabinet (GeForce2 running DirectDraw) the different is sweet bugger all. This is entirely a result of using 2D accellerated drivers on modern cards.
Test for yourself on your own systems, and see what the results are.