This is my first character with mysticism (why it is the best for munitions, I dunno...one would think thematically that would be Arms) - I have previously leveled characters on both Arms and Science.
I don't know if mysticism is supposed to work any differently from other skills, but I am getting no skill raises at all from harvesting.
My skill now is three - I got two skill raises from doing the opening quests (anti-rad and anti-cold) and have harvested a good number of nodes. I have not gotten a single skill raise from harvesting a single node.
Well I don't know how it is per level or anything, but in the early levels, you'll mostly want to level by Researching. You get 10 skillpoints per research. I think I vaguely recall not getting any skill-ups from harvesting either... But maybe that's intended, considering in the very starting areas you get 20 harvets in the same radar area, whereas in "real" areas, you'll need to travel a bit to find one harvest. It doesn't really matter though, you'll get to 100 skill in just a few researches. And after 100, I can say from experience that harvests give a bunch of skill-ups, while research only gives 2-4 at a time.
As for the thematical bit, I wholeheartedly agree with you, as I'm munitions myself. I would place Munitions, thematically speaking, in both Science and Arms. However, the NPC's are speaking statistic-wise. Which is a bit out-of-character and weird, but okay. Anyways, From what I gathered so far, neither of the crafts seem to be better for Muntions. I'm currently leveling as Mysticism, but my boyfriend has Arms. And contrary to Myst., Arms has access to a Primary Defense major that has Dex/Rec, something which neither Mysticism nor Science has. Also, Mysticism doesn't have access to Defense Minors with Dexterity, something which Arms does have. And both Arms and Mysticism have access to a primary offensive with Dex, or a Utility Minor with Ego. So, in short, I think that if you are Dex/Ego, you should definitely go Arms.
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As for the thematical bit, I wholeheartedly agree with you, as I'm munitions myself. I would place Munitions, thematically speaking, in both Science and Arms. However, the NPC's are speaking statistic-wise. Which is a bit out-of-character and weird, but okay. Anyways, From what I gathered so far, neither of the crafts seem to be better for Muntions. I'm currently leveling as Mysticism, but my boyfriend has Arms. And contrary to Myst., Arms has access to a Primary Defense major that has Dex/Rec, something which neither Mysticism nor Science has. Also, Mysticism doesn't have access to Defense Minors with Dexterity, something which Arms does have. And both Arms and Mysticism have access to a primary offensive with Dex, or a Utility Minor with Ego. So, in short, I think that if you are Dex/Ego, you should definitely go Arms.
I even switched crafting skills and went back and it still doesn't work.