Because we're using free resources for the IP to Flag mapping (and perhaps is a bit lax when it comes to update it)
some IPs don't show flags because there is gaps in the database of what region the IP belongs to. So not all "no flag" posters does it on purpose. Additionally having an option to hide your flag improves anonymity for users from non USA countries as there are often only one or few regular poster from those countries.
The option for OP to hide IDs on the thread was implemented so Anonfilly and others would not have to change their postinghabbits in those threads. This would make the flow in those threads stay unchanged.
When it comes to memeflags, to quote one of the users >>>/mlpol/186231
"They are legacy stuff from the founding, but aside from being a badge of an oldfag there are no meme flags."
Regarding TOR nodes they are already blocked. VPN is allowed, but we blocked TOR nodes as it opens up for too easy abuse.