Swiss cheesing it is really good for offroading if you hit water a lot.
If you go to my cardomain site, you can see movies of my truck hitting water 3 feet deep or so with no hydrolock. If you swiss cheese it on all sides from the bottom to just below the filter you then need water to rise on all sides to the bottom of the filter before you seriously ingest any water.
The proof is in the last several years of offroading at Wharton: people have gotten hydrolocked going through relatively shallow puddles, but I've slammed through very deep ones and been fine.
The downside is as mentioned above by Steven who has you doing it on only 2 sides: I get hotter air into my intake which can hurt performance. I make the trade willingly to be able to ford without as much worry.
But I still worry, so I'll be building a snorkel, lol.
I used a 1" flat "spade bit" like you use for boring wood. It makes short work of the plastic the air box is made of.