Go ahead, please be stupid.
Go to Project Options -> Compiler Options -> Custom Options.
In the memo type "-v0" without the quotes.
Now only errors (no warnings or hints) are being output by the compiler (and therefore shown in Messages window).
I've tested it and it works.
Then I deleted that option as fast as I could, because I am a lousy programmer and want all the hints and warnings to show up.
The command line messages don't bother me.
Lazarus IDE just pipes the "commandline" messages and filters them.
Bart