Having done a little further testing, it seems like Miria unequips her equipped weapon when asked to take off her armor. Looking at her dialogue responses, she responds with the dialogue pertaining to putting her weapon away (string 1600, used in Node1003 when unequipping weapons) rather than the one about removing armor (string 1009, used in Node1009), and indeed she'll remove her active weapon but leave her armor on.
To avoid triple-posting, I've actually isolated the issue. Decompiling mcmiria.int, on lines 2366 and 2369, as part of the block Procedure Node1008, which read unmodified as:
giq_option(4, 106, 9261, Node1003, 50);
giq_option(4, 106, 9260, Node1003, 50);
which calls Node 1003, i.e. remove weapon, should instead be modified to:
giq_option(4, 106, 9261, Node1009, 50);
giq_option(4, 106, 9260, Node1009, 50);
to properly call Node 1009 to remove armor. I've recompiled, and this works.