The specialized NeoGeo emus will do a better job. Keep in mind MAME was geared for accuracy, not performance. MAME32 might be a little slower than DOS or Linux MAME too, just because you have the OS overhead to deal with on a lower spec machine. I can't imagine it would make a huge impact though, unless your hard drive is grinding away which would indicate a shortage of RAM.
Using NeoRageX, for example, runs just fine on PII-PIII/K6 technology, and you can't really perceive a difference in quality over the real boards.