The rear BB is the lowest point, also, it should have ports to allow airflow and also water flow from the other tubes into the BB shell.
The FWD BB shell I do not believe has these holes on account of the eccentric. You will want to check this as it if there are holes, it could be where the water entered.
The other reason to keep the rear BB shell dry is that the bottom bracket itself will become corroded and could damage the threads when removed.
With your storage requirements, and likely the climate also. I would seriously consider removing both seatposts, both bottom brackets, the eccentric, and dropping the fork out. Flush the frame with clear water and dry, use a hairdryer to warm the tubes. Make certain it is dry. Locate some Corrosion X.
and coat the tubes interiors. Slosh if needed.
Action Tec makes an item called the dry valve.
This would give a professional means to add a one way valve to minimize your concerns.
So there is the high tech way.
The info below for drilling would be based on how much water came out of the frame.
As you mentioned drill holes and tape over them. For where you live and what the frame may see over its life, I would drill several 5 mm holes. Using a quality drill bit or better still a unibit, I would add a hole in the rear BB shell (lowest point and centered if possible. I would add one towards each end of the bottom tube (approximately 25mm away from the weld on the bottom centerline), I might even consider adding a hole to the lower end of the downtube.
Truth be told in all of this, you best bet is to stay on top of your maintenance, with frequent disassembly, inspection, clean and lubricate. While apart annually corrosion proofing the frame may be a good idea.
The holes will work and allow easy draining plus application of corrosion preventing materials.
Best of luck with it.