Two of those scenarios came from within Starfleet itself - wasn't an outside threat. Moriarty gained computer access due to the computer creating a sentient hologram capable of defeating Data... by its very nature it needed computer control/access to do that. Be'Lana's ex was Starfleet... and as we saw, he was quite adept at Starfleet computer manipulation - but then, any Starfleet officer with his intent would probably be able to do the same - VOY crew didn't resort to that because they weren't as desperate as the Equinox crew. As for the Klingons using a program... yeah, too bad they hadn't thought of dismantling the outer hull instead... would have blown up the ship while its at Warp or once it jumped to Warp. Or why not instead cause the program to go into the armory systems and blow up the Photonic torpedoes? would have likely been faster (and possibly easier). Having the ship consistently increasing speed until it blows up... meh... it wasn't a bad attempt, but out of different hacking attempts, that was not particularly good... it gave the crew time to fix the problem - and the program still had to have been installed manually (as opposed transferred wirelessly from their own ship).