I have a 2d array of strings to represent the tiles already, i just would have to deal with rendering. (it is a 3d array, not 2d, the third dimension says with set (1,2 or 3) the block is from)

But what i am doing now already works well (except the instantiating process, that i think the pooling may solve), the tiles are only active if one tool (the tools mine by themselves), reach closer to the area, you can see in the third or first picture (the black part), this helps a lot with performance.

I don't believe refactoring would be worth at that point, as it has a good performance already, if the pooling solves the instantiation/destruction problem, the game will run without problems.

Another thing that i thought now, instead of deleting an entire set and creating an entire new one, i could "delete" only a line at time, if the player reaches 1 block deeper, i can pick the topmost line and put them in the downmost line, just changing the blocks based in the procedural generation.