The recent hentaigana proposal requests that they be encoded as Standardized Variation Sequences of hiragana. This seems like a good idea, since fallback in the absence of font support would be to the standard hiragana, so the results would still be readable. But where does that leave the Kana Supplement block? That block contains only two encoded characters, but was allocated 256 code points, presumably for the future encoding of hentaigana. With hentaigana handled by SVSes, it seems unlikely that many of those points would ever get filled. I realize there's no shortage of code points in the UCS, but still.
One thing I noticed: the hentaigana proposal contains a duplicate of an existing character. MJ090014 (え variant with mother ideograph 江) looks like it's already encoded in the Kana Supplement block as U+1B001 HIRAGANA LETTER ARCHAIC YE.