I'm making an offering bowl for Nocturnal. It will accept gold, gems and jewelry right now but would Nocturnal value offerings of soul gems? She IS a daedra after all so I'm thinking yes but thieves might not want to touch items like soul gems and so not pick them up. Opinions?

I don't know if Nocturnal would be interested in souls, let alone material valuables, but I don't seem a problem with thieves handling soul gems. Thieves have different values, they're just all willing to steal. In later TES games, it's convenient and useful to consume lots of souls and there's no mention of the ethics around it, so I don't expect most pc's would care. In Daggerfall, it was considered cruel and the organisations that did allow it kept it quiet from the public.