So , two ways to set data tables/ windows to show / disappear are :
1. When you create them
2. When you have a handle / reference to the object .
For case (1)
dt1 = Open( "$SAMPLE_DATA/Big Class.jmp","Invisible" ); dt2 = Open("$SAMPLE_DATA/Air Traffic.jmp","Private") ;
dt1 = Open( "$SAMPLE_DATA/Big Class.jmp"); dt1 << Show Window(0);
Setting a window to private makes it hidden even in the list of windows of JMP - so this is more closer to your initial need. "Private" can also speed up your script . Hope this addresses you need .
You can apply the Show Window to a window as well.