The hose will be in the PVC holes so air should be able to escape easily.

Leave the pvc ends uncapped. Any air will make it hard to sink straight.

I'm not sure what you mean here. How would I attach cross pieces to the hoses?

Cable ties are easy and cheap.

How would making the center pieces a foot longer create a 3D effect?

Try to avoid a flat top (parallel to the water surface). Have the middle hoses stick up a foot more than the outside pieces. Irregular shaped structure works better IMO than cubes and boxes.