All, I believe it is safe to remove the crypt use flag entirely from the genkernel live ebuild and output the messages uncondissionally.
Created attachment 312107 [details, diff] genkernel-9999.patch Patch to remove the crypt use flag.
I am going to say no to removing USE=crypt because we try to keep various ebuilds in sync and changing this would require touching stable ebuilds. With that said, I have committed an updated metadata.xml to indicate the USE=crypt is obsolete.