Allowing boarding from either side of a single ship seems reasonable, but the real question then becomes how do you want to deal with multiple-multi-ship boarding events? IE: Player A brings two of their ships to either side of player B's first ship, then B reinforces with a second ship of their own... Should A be allowed to bring in a third ship? Should A be able to bring in a third ship and park it against their own to have its crew reinforce an existing attack?
As for dealing with capturing ships, I think that comes down to a crew management and risk management system:
- You can Sail a tall ship with as little as a half dozen people. You're not going to do it well, or respond to changes in wind all that quickly, and struggle to travel as fast as you normally could, but you could still get a ship back to port.
- Then there is the question of crew: Do you press members of the previous crew under your own command while capturing the ship? Do you put a half dozen of your men in charge as officers and sail the new ship with the old crew and maintain efficiency? Do you take some of the new crew onto your previous ship for lower level work to free up more of your existing crew to be moved to the new ship? How much risk of mutiny is there in either case? - How loyal is the crew and captian you've placed on the newly captured ship? (If they're pirates, then why not let them bugger off with your ship when you're not looking?)
If you choose to avoid the risks of an uprising from the old crew, what do you do with them? Will all your crewmen go along with the idea of just tossing them overboard, or could that cause unrest and raise a mutiny risk from your own crew?
Whether tossing them overboard, leaving them in boats, enslaving them, or dumping them in the nearest port, how do you manage the two ships with your current crew? Do you put a handful on the new ship and have it barely effective for anything more than getting from A to B (And struggling to do even that), or do you more evenly spit your crew, leaving more work to be done on both ships? Fewer hands on deck to man the rigging, fewer to handle the and reload guns, fewer to carry out the general duties to keep a ship in shape and well ordered, fewer men on hand to repel boarders... etc. Or maybe you keep one as a near skeleton crew to maintain the effectiveness of your main ship, but saddle yourself with a lagging pig you then have to protect if you want all of the cargo and such...
Or maybe you just strip the newest boat of anything of value that isn't nailed down and can be stuffed into your main, steal/dump all their shot and powder, and sail off with a friendly wave and 'thank you for the stuff'?