Sanpuku Seido states that you count Glory instead of Military/Political skill when resolving conflicts. Conflict resolution rules state that bowed characters do not contribute skill, but says nothing about Glory (which is not a skill and the card does not specify that the value is treated as a skill). Does that mean at this location a bowed character's glory will still be counted for resolution purposes?

Bowed characters do not contribute glory at Seido for resolution. There are a couple reasons why this is, but the easiest is that:

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When instructed to count a total of game values on a subset of characters, values on bowed characters are not counted.

From "Count" in the rules reference.