How secure is using TOR in Lightning Network?
The paper you link to when used as advice rather than a scholarly investigation into the tradeoffs of different choices is outright bad advice.

The attacks they give are largely generic and have little to do with tor itself, while use of tor provides non-trivial protection against many other vectors, and if used consistently and exclusively at least prevents linking the users network identifiers with their activity. Almost every security decision is an exercise in tradeoffs when it comes to advice you cannot just consider the risks of one option while pretending the alternatives are riskless.

Moreover, its not uncommon to see this article breathlessly promoted on the same pages that recommend users use lite wallets that simply send all their addresses to remote hosts-- effectively always operating under the worst case possibility the article suggests. If using tor is a bad idea then using, say electrum, is "holy crap why would you ever do that?!" -- yet you don't see that level of promotion against using electrum or similar.

Given the recent rise in promoting it I am concerned that some parties might be sharing it with the express intention of undermining user privacy.