Generally yes.
First, you want to fight at the optimal range of your weapons, so if you’re using different weapons you will use one of them sub-optimally.
Next, you want to use modules and rigs to increase the effectiveness of your weapon system. Better application, more damage and such. If you’re using different weapon systems, your modules and rigs only work for some of your weapons instead of all of them.
These are just guidelines, so if you can find a good reason to equip different weapon systems in a way that works for you, go ahead.