I was playing the ROM, and then I fighted the Shroobs Seijin, and gues who's the big unknow frozen thing in the background ? It's the Elder Princess Shroob !!! She, along with the Princess Shroob, can be seens frozen in the background before the fight. So, apparently, they aren't dead. But it's strange, because we seen the Princess Shroob exploding and the spirit of the Elder Princess Shroob exploding too. So, here are two theories:
-M&L3 happen before M&L2. The Shroobs weren't defeated by the Mario bros. and they took over the Mushroom Kingdom, but someone from Bowser's army freezed them and took them to Bowser's Castle. Then the survivors moved to another land because of all the destruction the Shroobs did and it's this new Mushroom Kingdom that we see in M&L3. Then the Toads repopulated and everyone forgetted what the Shroobs did.
-In a next game, someone will go in the past and save the Shroobs from the Mario brothers, but then froze them and take them to Bowser's Castle to study them. The Kingdom was then reconstructed and never changed again. Then the Toads repopulated and the Shroobs invasion is a history fact, and none of them survived.
In any case, we can be sure that if Nintendo make a M&L4, the Shroobs will be the main bad guys. M&L1 had Cackletta and Fawful, M&L2 had Shroobs, M&L3 had again Fawful. Also, this thing would be awesome. Maybe that the two timelines are always inter-changing, who know ?
So, what's your theory about the Shroobs's surviving ?