I can say for sure that the greyed-out Identify is because your thief/mage is still wearing armor. I occasionally have that happen to me, too, when I forget to take the armor off my T/M, bard, or whatever.
As for the bow-removal bug, take Roboghost's advice. Now that I think about it, I can remember this happening to me before, but it's pretty infrequent.
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