I have a 3/4" spacer under my holley on the dual plane manifold which came with the ZZ4 crate engine. The spacer is the plate for the nitrous system. I have a drop base open element air cleaner with a 3" tall filter element, and I have no hood clearance issues at all. A four hole spacer will help to straighten out the air flow, especially on the "short" side of a dual plane manifold and will help with throttle response.
If you are concerned, try it, place some 1" tall play dough pyramids on top of the air cleaner, carefully close the hood, then open it and see how far they have been compressed, that will tell you if there is an interference issue.
Hope this helps
Cheers
Richard