Yes, this can be an issue for the design of your H-infinity controller using "hinfsyn". The "hinfsyn" function requires the correct number of control inputs to design the controller properly. If "sconnect" is returning a system with all inputs (control plus exogenous) combined as control inputs, this will mislead "hinfsyn" into considering all inputs as controllable, which is not the case.
You should manually specify the correct number of control inputs (which is 6 in your case) when calling "hinfsyn". You do not need to "overwrite" the number per se, but rather ensure that when you construct the system to be passed into "hinfsyn", it correctly reflects the number of control inputs and measurements.
Hope it helps!
Regards,
Soumnath