I don't know about 800 games. I narrowed a list for vert, single player, 4-way, 2 buttons to be roughly 100 games. I have a whole disc set up and ready to go for that at home. First off, I can't bring myself to dedicate a good computer to a 4-way vertical machine, so arcadevga is out due to no agp slot. If you have a pc with agp to use, then more power to you.
The cost of the 48-1 has dropped drastically and still is dropping. The price point is becoming negligible in choice. Lets put it this way, you can get a 48-1 for less than an arcadevga/jpac right now.
Setup wise, the 48-1 wins hands down. If you have jamma, you plug it in, and go thru a quick set of setup screens. 5-10 minutes and you are done for good with setup. In your case, you would need to address the fact that you don't have jamma - but a nintendo wiring harness and a Nintendo monitor. So it won't exactly be a plug and play environment.
If you go simplistic, MAME can be set up fairly quick, but front ends can be a pain in the ass to set up. you also have to sort and trim a romset, download software, set up software, blah, blah, etc.
Long story short, it is really your preference. With a Nintendo cabinet, the setup will be about the same either way.
I can also give you one last point of interest. The resale value of a cabinet with a 48-1 is higher than a cabinet with an old beater pc in it.