But as your screen is flat and mouse input is in 2D, it makes sense that everything is presented to the camera in a way very close to 2D.
That what you see is a 2d projection is a necessity, since the display is 2d. Not a necessity of the hid.
In a 3d game world you typically move around. And this is done with a combination of inputs. You use several input devices or at least several commands. The mouse usually does left and right and up and down. And a command does the forward motion. That is enough to fully navigate in 3d.
What your game probably has, is a point&click interface. That input area is of course 2d, since you move the pointer in 2d. But you could minimize the interface even further and eliminate the pointer, using only selectable highlights the player can navigate between by pressing left and right. Those highlights could be presented in a 3d environment, while the hid is basically 1d.
But at this point, we could extend the OP question to real time. Why is so much on Itch static gameplay, instead of real time. On second thought, there are lots of platformers and all those rpg maker games.
(And the answer is of course the same. It is easier to do.)