Hm, an interesting detail that I might have overlooked when making Astroponics an optional technology, rather than a required one.
The Astroponics tech (unlocked at the same time as the planet discovery techs) should allow you to grow trees in space. This technology was originally required for planet discovery, but didn't seem important, so I made it optional instead; this may have been a mistake, since I hadn't considered the new ammo recipe structure.
I might actually have to revert that change, since it does appear to be a soft requirement for space travel (excluding the starting moons, which should be asteroid free paths).
I vaguely remember one of these mods (either Lignumis, Astroponics, or one of the other "Wooden" related requirements) having a setting to disable wooden ammo.
As an alternative, I can also offer the Lite version of this modpack, which is more focused around player usability (whereas this one is mainly just for dev compatibility testing). That version of the modpack makes Muluna and Lignumis (and some other unimportant planets) optional instead, so this wooden ammo recipe thing wouldn't be an issue (though it sounds like your save might be a bit too deep for that, too many requirements would need to be removed)