Yes, the obvious place to check is water invading any cracks in the ignition leads to the spark plugs. This can bleed off the spark to ground before it reaches the spark plugs.
I had this nagging (poor running in the rain) problem years ago on my 74 CB550. When it was dry out, the bike ran fine. So, as a test, I drenched the ignition leads with a water hose one at a time, only to find the bike ran without so much as a hiccup. Puzzled, I made no changes, only to have the problem reoccur the next rainy driving day. Fed up, I pulled under an overpass, removed the tank, and hand dried all the ignition wires and coils with a rag, only to find the problem still there. So, I stumbled the last few miles home where it finally occured to me to check the points. Sure, enough, with the points cover removed, I could see water bridging the points. I dried all that out and the bike ran with it's usual dry day zeal. In the months to come, I also I also found out that, if there was water in there, the engine's heat would turn it to steam, and redeposit water condensate throughout the compartment and cause odd engine behavior for a few days after the rain. Further, I learned that the stock cork points cover gasket was, at best, good for one installation/compression cycle, and would leak when reused. It seems that the cork would shrink on the dealers shelf (or was cut wrong during manufacture) so that it wouldn't seal the points cover even when new. So, I went to the hardware store and found some neoprene sheet of the size and thickness comparable to the cork ones. At home with a #11 Xacto blade, I carefully cut out the neoprene in the shape required to become a points cover gasket, and installed it on the bike. That ended the engine run problem in the rain. And, as a bonus, that same gasket is reusable and still on the bike working to this day. I now make a neoprene gasket for each SOHC4 points cover I own. I also learned that with reliable power coming from the engine in the wet, it really pointed out the poor front brake preformance. But, that is another story...
Cheers,