I found a workaround that I wanted to share
% check if Simulink was started in the past
current_licenses = license('inuse');
if strcmp('simulink', current_licenses)
% code that calls findsystem
end
It is not the nicest way to check if simulink has been started in the past by checking the currently used licenses on the machine - but it works most of the time.
Attention: by doing this you will not catch any timeouts that might occur when you are using a server based license.