Can online servers read my /minebot commands?

No.

Minebot commands are intercepted by minebot. The server admin will not see any commands starting with /minebot or /minebuild. It will however see mistyped commands (/minebt).

It is possible to intercept tab completes of the first word, so if you type /min<tab> often the server owner might get suspicious.

In late 1.7 versions and in 1.8, as soon as you typed the first space after /minebot, you can safely use tab complete. It will not be sent to the server.

(PS: I'm the minebot author ;-))