First off, it's not just privacy but also issues with custody on lightning.  Most people aren't willing to spend the time or money (or can't afford) to self-custody lightning.  We documented the issues with custodial bitcoin in an earlier post with Hayek.  And how it mirrors problems with the fractional reserve banking system.

Second, regarding this situation, they were able to rule out Monero outputs by running malicious nodes, but those outputs had no meaning if it stayed within Monero itself.  As soon as someone swapped it for Bitcoin at a business that can be given a supenea, then it is a lead, and in this case, got a vendor doing XMR->Bitcoin in colombia.

If they are running that many monero nodes, they are running that many lightning nodes, and custody is a huge issue then