Of course the owner can allow his CHL employees to carry even though he has a 30.06 sign. Remember, the employees are in his business. He sets the rules. The 30.06 sign would apply to customers or non-employees.
Keep in mind that the 30.06 sign pertains to trespassing. It is the formal notice not to carry in the business without the owner or representative having to actually tell a customer a gun cannot be carried onto the premises or the customer will be trespassing. Also, since it is a trespassing issue, the owner or his representative will have to call the cops to enforce 30.06 if the customer does not comply.
Note that employees are not trespassers.