There are two ways of doing this.
I could create a script that can run your bat file and hide the console when it runs the bat file. This is the harder way.
Or in about 3 minutes, you could learn how to use autohotkey and do it yourself
As i'm a nice guy, here you go:
In ahk, the code you're looking is something like this:
Run,THENAMEOFYOURBAT.bat > FILETOSAVETHELOG.log,,Hide,
This code will solve your problem, and will only display an icon on the bar for less then half a second, hardly noticeable, and no window.