Mastery of Resonance gave Zenos access to some very Ascian-like abilities which were almost 100% definitely a sort of magic. He never demonstrates "conventional" magic, like say casting spells, but he also wasn't trained as a mage. His applications of aether were always far more direct. Many of these abilities did not make a return in Endwalker for unknown reasons.
Not crystals. Those swords were themselves enchanted, and he most likely used Garlean technology to further augment their capabilities/his techniques.
Hien states, and I quote,
"Magic? With a Garlean body? That's hardly fair..."
This is said in response to Elidibus doing something blatantly magical without calling upon the unique properties of Zenos's arsenal. He emits a shockwave that immediately defeats those assembled to face him. Prior to that he'd been utilizing other blatantly magical skills, also without utilizing the weapons' enchantments. He started out using Zenos's skills, but after a while he was forced to start mixing in magic.
https://youtu.be/_yvCSDrAWCw?t=189
Here's a YouTube video for reference. You can see here Hien reacts rather vocally upon first seeing Elidibus start pulling out the stops. While he did involve one of the swords here, that was not one of Zenos's techniques. It's also distinctly different from the enchantment we know to be on that particular weapon. You can see other, more blatant examples of outright magic both during the fight and in the following cutscene.