The reason you can't get the simulink using the same methods as , is that its actually a DAStudio object, rather than a java container.
That said, in 2013b I'm able to change the name of the simulink window using
aStudio = DAS.Studio; %Get a blank studio;
allStudios = aStudio.getAllStudios; %Find all the studios currently open
allStudios{1}.getStudioTitle %This is the current name of the first studio
allStudios{1}.setStudioTitle('This is the new Studio name')
I don't know if the calls change in later/earlier versions, so you may have to mess around with it yourself.
In addition, most of the credit for this answer goes to Yair Altman & Donn Shull