[gioele]

> I don't know how they're encoded on their database.

All hentaigana are available in Unicode 10. They can be found in the Unicode block 1B000–1B12F (Kana Supplement + Kana Extended-A).

For example, U+1B004 𛀄 HENTAIGANA LETTER A-3

[phonon]

They're not in JIS X 0213, so don't expect them to be widely available any time soon...