I usually find myself at a point where I'm placing one weapon and two defenses fairly early on in the game, usually starting with 4 attack and 4 defense on a small hull, and those are the first ships I make in any significant quantity, so I don't consider the difficulty in fitting two defenses on a ship a major factor.
I also don't bother with tiny hulls, there I think you'd have to be fairly well along in the game before split defenses were feasable.
As for splitting my research, I agree, and even mentioned that in passing. However, there's a penalty in overly specializing in a single weapon/defense tech line as well, so even if the split defenses weren't beneficial, I'd still be researching different tech paths. When I don't, the bit of any war immediately following the AI adapting to my current ship designs is usually quite painful until I research the right weapons and defenses to adapt to the AIs new ships. It's painful enough waiting until the ships start rolling off the production line, but getting stuck waiting on research before you can do that as well?
As for your last comment, are you saying you would never split weapons on a ship, or never split weapons research? If the former, I agree wholeheartedly, if the latter, I have to disagree there as well. The AI usually (but not always) adapts to your ship designs. If I sit with a single weapon type too long, I'm soon facing ships where the corresponding defense makes up the bulk of the defenses the ship has, and I'm getting taken to the cleaners by an AI that by all rights I should be beating. Improvements in the AI will only intensify this factor. On the other hand, if the AI seems to be stuck using the same wrong defenses (which I have seen at times), then by all means dig deep in that one weapons branch, just be ready if it gets unstuck or someone with the right defenses joins in.
Just realized one other reason that the split research doesn't impact me as much as it might impact people with a different playing style. I'm the tech leader, period. Oh, sure, for the first few years, I may not be outresearching the rest of the galaxy put together, but it's only a matter of time, and even then, I've probably traded for any tech that any of the AI players get (except medium hulls, they're very protective of that one). Those 4/4 ships I mentioned? I'm usually doing that before researching ANY military techs on my own. The AIs get very stingy with the higher level military techs, but depending on relations, you can usually get second generation (mass drivers, harpoons, etc) military techs out of the AI with suitable non-military techs. Sure, you'll be trading a tech for one that took a third as much research to get, but you're trading it to several AI players, so it all works out in the end.
Besides, some techs are just to good to keep to yourself. Nothing ensures a galaxy full of war quite like selling the "Alliance" tech to everyone in it, even if you're only getting 100BC for it from the poor races