I have to retract what I wrote previously.
I bothered to try DSDoom SVN again on my DSi XL (SD-slot, TwilightMenu++) and to my amazement found that it works.
Not only that, I tried one of the most demanding wads, Freedoom1 (placed in the root of the SD) by editing the PrBoom.cfg file and, not only does it work perfectly, but it seems to be able to save without the game crashing.
I've tried saving 8 times in a row, in different points of the game, up to map 3 and it has never crashed.
Incredible discovery !!!
@KirgoPlayer007 For you, I suggest to delete the game saves; if it still doesn't work, delete and copy the Prboom.cfg file again.