You can, and many have as part of retheme projects. The problem is in when the sounds are played. The music and sounds are generally event driven. Most sounds from a pinball aren't music but simply sound clips activated by hitting various targets, starting/completing modes, etc. On many machines there are background sounds - whether it be a repeated sound-effect clip or a song. Its really only these background sounds that you likely want to change. Depending on the game there may only be one or a couple background sounds/songs, so you couldn't replace a whole bunch.
Generally the replacement boards would take in the various trigger signals in place of the OEM sound board. it would really depend on what machine you're starting with and the sound solution you pick as to what you would be able to do.