Landing struts have an option called "Deploy Shielded", which controls whether they can be extended while inside fairings or cargo bays. This is a confusing name, especially since toggling it in the editor seems to do nothing, and it only takes effect in a specific situation that you might not encounter while testing.
I think it should be renamed to "Deploy While Stowed" or something similar, which would make more sense and match the warning message: "Cannot deploy while stowed".