Heavy use of wireless networks can definitely cause slowdowns, up to the point of failure/denial of service. The WAPs or your NAT router may simply get overloaded.
 I understand your question so that the employees are sharing the Internet with the outside and install software without authorization. [/edit]
First, you'd need to establish a reasonable usage policy for your network - what users may do and what they definitely mustn't do. Then you can configure or upgrade your network to enforce that policy.
Since we know nothing about your network and product recommendations are explicitly off topic here, we can't provide much help with the upgrade unfortunately. If you add the relevant information to your question (a network diagram and the device types/models) we might be able to give you some starting points though. Note that consumer-grade devices are explicitly off topic here, however.
It might also be a good idea to hire a seasoned (and independent) consultant at this point.