Just like Cultivation/Taravangian, who's playing who, I'm split on Hoid/Taravangian too. On one hand, it seems a theme of the book that even immortals make mistakes, on the other hand, Hoid could be misdirecting Odium. I mean, at first the epilogue seemed to be Brandon's opinion on writing, lol but yeah it is totally possible that Hoid just misdirected Isshin because otherwise what would be the purpose of him meeting with Odium?
It makes sense that Hoid used Breaths to store his memories, it's the easiest Investiture to acquire and integrate but it's also more Physical, more attached to the person than their Spiritweb. Think of it as being welded rather than melded. That's why Breaths are so transferable.
Did Hoid really not think of their vulnerability? He has access to a lot of different Invested Arts, and he's quite old and learned, he might have copied his memories over to the Breaths specifically for this purpose.