Baseline Star Trek, before any of Joe's other perks and upgrades, can pretty much do it by itself. Or at least close enough. Add in the other tech bases to fill in any gaps, all the upgrade and masterwork perks, the better materials, magitech integration, the more conceptual/divine abilities, his current and future existing infrastructure (Like his soon to be spiritron computer (which pretty much exists for this purpose in it's source material...) for unholy amounts of processing power), etc. and something that can live scan a planet would be child's play. Alongside other tech and abilities that can hide it away and make it effectively undetectable; How ridiculously hard it would be even for Zion to detect something Joe used his everything to explicitly hide away.
Though, Joe doesn't have our meta knowledge, and can't be certain he really is that ridiculous. Especially with his passenger telling him things like killing an endbringer would cause something bad, or that Taylor is important for dealing with a problem worse than the endbrinngers, giving him a pretty good idea that there's some unknown out there of unfathomable power. He doesn't know it's Zion, let a lone what Zion can do, but he knows enough to not take unwarranted risks that could trigger a threat he might be unprepared for. Risks like a powerful scanner ferreting out the secrets of the world that could only be detected by something on par or beyond Joe himself, and thus possibly drawing that things attention. Hence the baby steps, like local stealth sensor drones, to grow more confident in his ability to go undetected before going to things like overpowered subspace satellites or something.