That's what bonnet vents are supposed to be there for. I've seen a set up like that, that was set with a magnetic catch which closed the vent when it was raining.
Other wise I think you'd be more worried about spray going in the filter and then once wet enough into the engine rather than sucking up water like a straw. If your using that A/C style flexable piping as you feed pipe I think it would collapse before it sucked water like that.
If you make it all fairly vacuum tight, then wont it just stall when going through water? Or do you just make the setup in such a way that it can suck in air from alternate sources?
Also, as mentioned before, if you put an S-bend in your piping I don't think you would have to worry about water spraying into your filter. I would be more worried about water spraying into the bonnet vent induction setup.
Lambolica, how did that vent close? Swith inside the car? Or did it have some kinda rain detectors like the Jags do?