Very few of them got banned, mostly for hosting raids of unobtainable species. This happened after the Zeraora raid event last year, when we suppose they added some Raid telemetry.
I suggest to get rid of any glitchmon, they can be detected by HOME and cause issues. In the past HOME would crash by detecting it. Now the application should work regularly, but GF/TPCi can still ban you, if they decide to.
As of now there are no known bans for altering a SwSh/LGPE save files with PKHeX.
Still, they can ban if they want to. We know the telemetry is there.
In the past generations there were bans reports for save files with unobtainable editings, hence the suggestion to only do legal editings.
Until now, no ban has been ascertained for the use of these tools.
Bans mostly happens for checks within the games server. If playing online, never use someone else savefile that has been online at least once, never use unobtainable character/items/things, only do legal edits. This applies to any game.