First I assume the games use the SDAT sound format, if it gets extracted with VGMtrans it probably does but most of the rest of this will be assuming that is the case. Also being a download play game you will need either an injector to run it as a normal game (I think there is something, never really had cause to do this though) or a flashme modified DS to get around the signing. If it is SDAT it should be uncompressed too which is nice.
About the only tool I really trust to make lasting changes to SDAT files is tinke ( https://code.google.com/p/tinke/
, not sure where latest builds are at right now), even then I tend to favour doing things manually with everything else being used to direct me where I am going. That said VGMtrans got picked up by loveemu last year and it might actually be better right now, you will probably have to build your own err build though.
1 and 2 would appear to be the same thing at first though I will treat them as different.
1) SDAT is a software drive audio player and a fairly high level one (hence most of the hacks working as they do), if you could attack it and get it to feed a different track request you could do a lot. I have never tried this on the DS.
2) I do this often enough. The basic trick is either to replace the song with tinke or swap the pointers so the original track points to a new track. Some games will have a different sound bank to handle different songs, I doubt a download play game will do this but theoretically the overhead is not that high so it could happen.
3) In some ways this might be easier than the music hacking one. I did just such a hack for one of the nanostray titles (bonus is it used SDAT but a slightly nonstandard version). Anyway along with pointers for everything there is a section that covers audio volume for all sorts of things. Stick this down towards zero and you should lose the sounds they deal with, you could tweak things in track level as well I guess. I believe it is slightly different for SSEQ stuff in case you end up reading what I did for the nanostray hack.
4) Brings us back to 1) really, though I guess you could instead use a cheat activator if you prefer.
5) I have never really had cause to do something like this -- most of the time save functionality being added back in is for games that lost it between beta/coding and the final game or between regions and this rarely happens on the GBA/DS. You would be making use of the fact that flash carts will support saves as saves go over a standard bus, you may or may not have to figure out how lfash ca. The absolutely crazy method would involve some ability to write to the flash cart's SD card but let us not go there right now.