Well, if you already have a hole there, I'm not sure that having plumbing there adds much of a burden or risk.
How to cap, if you decide to cap, probably depends on whether you plan on using the bulkhead in the future and whether it's slip or thread.
The safest way to cap a bulkhead, would be to use a slip bulkhead and use pvc primer and cement to put a smal length of pipe and a cap on either end. If you do that, though, you can't use that bulkhead in the future. It's just a cap. You'd have to drain the tank and take it out to use it.
If it's threaded, the way that would provide you the most options in the future is to buy threaded caps and screw them in, using teflon tape on the threads. That way, if you want to use the hole in the future, you'd just have to remove the caps. On the tank side, I might do this by getting a male adapter, and cementing a short lenght of pipe to it, and then cementing a cap onto the pipe. The advantage of doing this is that it will stick up out of your substrate a little, so it will be easy to find if you ever need to get to it, and you'll have a better grip on it to unscrew it.
If you have a slip bulkhead and want to preserve your options, you'll need to cement in a female adapter, I would think.
Note that you don't need to plug both sides of the bulkhead. You could get away with just doing one. I'd do them both though, for a couple of reasons. First, as my last post makes clear, a little redundancy seems worth it when you just spent the weekend almost putting 100 gallons of saltwater on your floor. Second, it will be easier later. If you decide you want to get to the underside later, you can just unscrew the plug on the bottom and work your plumbing without having to do anything up top, since it will already be plugged.