I think I am using the cleanup tool wrong cause either it does nothing or it collapses the whole model. So in the end smoothing and looking for strange bumps was the best way for me to find extra vertices.

This is perhaps more of a philosophical question, but do models have to be perfect or will they render just as good if one piles up a number of different "boxes" that intersect? I mean you could make a T-shape with extrudes that are connected or simply stacking two qubes? Does it matter in the end? Assuming you will not animate the object?