No explanation's given in the Epic Level Handbook (195), the Update Booklet, or the SRD for the ha-naga receiving that +10 to its spells' saving throw DCs.
And, to this reader, it seems that the ha-naga, as written, receives that substantial bonus to all of its spells rather than only to those spells from the domains Chaos and Evil. That is, the ha-naga's spells description says
Ha-nagas can cast spells as 21st-level sorcerers, and can also cast cleric spells and spells from the domains of Chaos and Evil as arcane spells (save DC 33 + spell level). The DC is Charisma-based.
Further, while the ha-naga spells description in the Epic Level Handbook omits the final sentence, it's otherwise identical. The ha-naga, it seems, is naturally, repeatedly, and inexplicably awesome at spells.
(Although straying significantly beyond the texts and inviting speculation, keep in mind that it's entirely possible that the ha-naga's enhanced saving throw DC is just a repeated error—mistakes
happens happen both in the Epic Level Handbook and the SRD's nominal 3.5 update of its epic monsters. I've posed a question or two about the demilich and a question about the leShay myself after trying to use those creatures as written.)
If those save DCs are too high, consider instead the Faerûnian ha-naga
Serpent Kingdoms describes the Faerûnian ha-naga (75–6) that largely possesses traits identical to the original ha-naga except that it has DR 15/epic and that the saving throw DCs against Faerûnian ha-naga's spells are computed normally (i.e. DC 23 + spell level). This might be a better choice to throw against a party of PCs with less than stellar saving throw modifiers.