Here in 0.99N8, shadowbat bootypedia page says it uses 2x missile slots and 2x shatow tech, while it actually has n. 1 lt/dv, n. 1 heawy weapon, n. 1 misisle and n. 1 shadowtech. Maybe a quickfix patch might deal with it?
Your screenshots show Snake, not Shadowbat. Snake indeed is armed like you describe.
As for upgrades, since the M-versions of the game it has been entroduced the ?captain who? in order to allow a more custom game experience, but it happens in the very early game, so if you're upgtading from an old save you will miss it, but actually during the game if you do something - i don't know if it a random event or not - you will get a "nihilist captain" event window and soon after the one regarding the captain who test. So the related window l pop up anyway in geoscape or there is something specific player has to to to triger it in case it never happened? The time is jan 2602, every such month it will happen?
This event always appears randomly if you don't have idea: faith
Edit: attached an updated saved game, (source L2 development branch here) so i researched airtruck but cannot buy it, but im able to manufacture it, since it apears in the production screen (no screen sorry)
Working as intended, it's a manufacturable craft.