Beatrix defeated several Vipers who owned Hanzo swords (O-Ren's, Budd's she found when fighting Elle, and Bill's are three I can recall right now).
Why didn't she take either of those? (the scenes after defeating O-Ren and Elle clearly show her walking away with just her sword).
I can see at least 4 reasons for her to take the swords:
Respect for Hanzo work. Leaving the sword to Muggles would be disrespectful to the master.
Monetary value. Clearly Hanzo swords are extremely valuable and rare
Backup weapons if she loses her own Hanzo sword.
Trophies (Elle planned to take Beatrix's).