No, Adblock wont actually affect MD, nor will prettymuch any of the blocking ones since we dont actually have any content that is blockable. The only issues comes when people use noscript and block stuff like off-site scripts, but they again will encounter a load of issues and probably will realise this.
If you start individually blocking elements of MD, then I cant really debug your specific problems. This is due to an issue last time when someone "bypasses" cloudflare, and when we changed IP they couldnt access it. I wasted a load of time trying to fix it for them and then they realised they had done this, and that was the reason. I might have a look, but you just open yourself to issues when you start deciding what you are going to block on MD.