There isn’t a centralized directory managed by the Tor Project. Instead, it’s more of a distributed hash table formed by every relay with the HSDir flag (currently 4776 of them, metrics.tpo shows only the first 2k).
To answer the question in the title, no, onion addresses aren’t visible to those HSDir, even though they are storing the descriptor. They only know the blinded public key, which can’t be tracked back to an onion service address (but knowing an onion service address, it is possible to compute this blinded public key). This is one of the improvement of onion service v3 against the now disappeared onion service v2 (which had shorter names).
And for the question in the message: to remove an entry, you’d need to convince/compel the operators of these relays (which are numerous, in numerous jurisdictions, and possibly not publicly known) to stop serving directory requests related to that onion service (and you’d need a modified version of tor that supports doing just that). Relays that comply could also be at risk of being considered as Bad Relays, given they don’t abide by the rules.
So removing onion services isn’t strictly impossible, however it is impossible to Tor Project, and would require cooperation from the majority of relay operators.
If you want to make this kind of things ever so slightly harder to pull off, you can learn about how to become a relay operator.