I have been using COtobo for a long time and have 5 clients open most of the time.
The thing to remember is that if you are silly in the way you use COtobo or CO Partner you will get jailed.
I don't thing TQ link accounts...... YET. So if one player gets jailed you should not find your other accounts there too.
I found myself in BOT jail a few days ago because I was stupid and forgot to turn off Ore Dropper before I left the mine and when I went through a portal COtobo kicked in and dropped some ore and bang I was in Jail.
Things to remember are once you finish mining turn off DC on players and ore dropper BEFORE you scroll to a City or use a portal. And don't drop items when jumping and you should be fine.
As for them checking to see if you have a multi-client enabled EXE there is no way for them to see that right now. Not legally anyway.
If your worried about it stop the auto updates and only update a few days after "Official" releases manually.
To stop auto updates edit your
version.dat file in the install dir of your game make the number much higher and you will not update.
Other than that you should be safe. Just be sensible