If I am playing a deck that has Alolan Dugtrio whose ability increases your opponents retreat cost by 1 energy, does playing Team Aqua Base increase their retreat cost by another energy (2 total)?
It normally depends on the effect but in this case, both cards say [C] more so to me, this is a additive effect and would stack. Of course if the Pokemon had a Float Stone attached to them, then their Retreat Cost would still be zero, since Float Stone sets it to zero as opposed to just removing [C] from the cost.
They definitely stack and that stacking is the basis for a fun SUM Sharpedo deck. In fact, if you get 2 Alolan Dugtrio down, it would stack 3 on there. As other posters stated, float stone, fairy garden, etc. all reduce this down to zero, so you can't necessarily bank on the effect always sticking a pokemon up top