The majority of games mame emulates output only two sound channels, closely followed by a number of older one channel games. The fact that nearly all arcade systems only have a left and right speaker setup (barring mostly sit-down games where there are speakers behind your head, and sub woofers which found their way in somehow), a 5.1 speaker system would be a little overkill on a stand up arcade - not to mention that arcade quality speakers usually means blown or dodgy rigs, emitting grungy garbled sound that most arcades are well known for (and loved for mind you).
But hell, do it anyway! If you can get a 5.1 setup for a good price just bung the bugger in there - you can always find uses for it later - and it will still give you great sound on anything you wanna play, just not arcade (grungy) perfect (but arcade quality sound ain't that great anyway (most of the time)). I recommend you put the L M R speakers under the marquee, and the rear speakers under the CP with the sub.
(P.S. Never play mortal kombat without a sub woofer!)
(P.P.S. If you end up deciding on a pedestal style setup with a big f.off rear projection TV, then a 5.1 sound setup is a must!)