I have glued acrylic before, as long as the glue is applied evenly, it will look fine.
What I had tried before was just glueing in dots at corners of large pieces, you could see the glue at the perimeter edges of the glue dots. On smaller pieces I applied glue on the entire piece and could not "see" the glue. It may be difficult to get a completely clear piece laminated together if it is a large window.