Probably the most common benefit is that momentary soft switches are typically more reliable than 3PDT footswitches, they also don't have the loud mechanical "clunk" of some 3PDTs.
For me, it's all about added functionality. Microcontroller-based relay switching opens up a whole new world of possibilities that aren't reasonable (or possible) with a standard mechanical footswitch.
Just to name few...
You can do the latching/momentary trick. (Intelligent Relay Bypass module)
Multiple functions in one footswitch (Hold the footswitch to increase reverb dwell to maximum, etc)
XOR switching of multiple effects in one enclosure (One stomp to activate effect #1 while instantly bypassing effect #2 and #3)
Microcontroller-based switching is an integral part of the upcoming VIIB project, it wouldn't have been the same without it.
The only negatives I can think of are added cost and slightly higher current requirements.