you can shorten the bottle to fit your needs... so long as the top and body fit together snugly, and the shrimp has room to fall into the bottle to get the bait as opposed to standing in the opening to get it.
Also maybe try sucking him out with a gravel vac? put some mesh in the top of the vac so he doesnt get sucked into the hose, but you should be able to create enough siphon to keep him suspended in the tube until you can pull him out to the top