I would expect the generic tunes to replace the song; they'd have to get the rights to every song used, and they couldn't do it (or didn't bother) with the Mario releases, I don't see them doing it here. Much higher profile television shows have had liscenced music replaced in the DVD, so I don't think a cult cartoon show is going to fare any better.
That said, I'm surprised and delighted this is finally coming to DVD. I thought that, if nothing else, the multiple liscencing issues (Nintendo, Capcom, Konami, Square, etc) would've prevented this from ever happening. I haven't really seen this show since it originally aired, and before Cartoon Network started catering to anime fans and "adults," my little heart hoped that the network would reach back and bring back the Nintendo cartoons.
Just last week I watched an episode on YouTube (albeit in terrible quality), and the nostalgia and the cheesiness made me yearn for the good old days. The cartoon portrayed so much so wrong, but its heart was in the right place. And some of that wrongness is so bad it's good--I would love to see the Captain N version of Mother Brain resurface in an actual (non-canon) game, like the boss of the next Smash Bros.