Kudos for actually calling these things “cylinders” rather than pistons! While most in the forums don’t seem to care, I think our students are done a disservice by not learning industry-standard terms.
Now about the plugs: The unused fitting in the pneumatic cylinder is indeed left open. In industry, we would at least screw in a muffler to dampen the sound (big cylinders are noisy) and to keep it clean inside, but these are not legal vex parts
On the solenoid, however, if you are using a double acting solenoid to run a single acting cylinder, you’ll need to plug the unused output port. You can choose what port to plug, based on whether you want pressure in the inactivated state or the activated state (this is the advantage of running dual-acting components as single-acting). A plug can be made by heating a piece of tubing with a heat gun while pulling/stretching/twisting it to seal it closed, or you can buy plugs like these: http://www.smcpneumatics.com/KQ2P-04.html which were included in pneumatics kits years ago, so should be legal by the “grandfather” rule.