I'd point out they have to be uninhabited if I hadn't been unable to mine on uninhabited desert planets as well.
Unsure how many are affected (have been able to mine water/volcanic but not jungle if I recall), probably quite a few.
As an aside, aren't the relations between various sources of mining strength kind of crazy? Take three instances: a pod wing, a shepherd and a mule.
The pod has no inherent bonus to mining, has either 1.5-6 (does each fighter's laser count?) strength and takes 3 logistics, providing 0 cargo.
The shepherd has 10 strength right off the bat, can be upped to 11.5 with an extra laser and takes only 1 logistics providing 100 cargo.
The mule can have 10 strength with a mining blaster, is actually dangerous (if terribly slow) and takes 3 logistics providing 250 cargo.
About the only perk to pod mining is the lessened elite crew requirement to get high yields (terrible anyway unless 6 per wing), but the ideal mix seems to be somewhere between high density shepherd/moderate density mule and all shepherds, both cases being backed up by several atlases. While mules with atropos racks are a pretty good stop-gap, something to be said for a billion borer drones.
Pod wings on the other hand are useless in combat and take a tremendous amount of logistics for what little they do, comparing unfavorably in almost every conceivable way to those two prime alternatives (and weird sh#$ like 2x tachyon 8x mining blaster paragon SO MUCH FLUX). They could make up for their heavy logistics/zero cargo/zero utility by having very high strength instead (necessitating atlases which is a horrible fleet to get attacked in).
Haven't tried mining shenanigans with any mod factions yet so can't really comment on the whole picture, but I did find it incredibly cute how you gave the junk pirate capital a use beyond 'mirv sponge' or 'lodestone'. Kind of liked the longer mine time though..