Sounds like a good reason to build a belly pan!
Soon after I got my first Subaru Legacy, I was driving through about a foot and a half of fresh snow. A lot was coming up over the top and I was swimming all over the road, but I didn't dare stop, because I knew I would be stuck in the middle of nowhere, possibly for hours waiting for a snowplow to come by. When the CEL came on I was really freaking out, but I kept going until I finally got to where the road was plowed and I could stop and check. The engine compartment was packed with snow that had come up from underneath. When I got to work and the snow had a chance to melt out, everything was OK and the light was off.
I'd check further before drilling drain holes, and definitely make sure they don't drain into the valve chamber.
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