Each named pipe created in Windows uses some system resources, which means there is a practical limit on the number of pipes which can be created. See:
Every time a named pipe is created, the system creates the inbound
and/or outbound buffers using nonpaged pool, which is the physical
memory used by the kernel. The number of pipe instances (as well as
objects such as threads and processes) that you can create is limited
by the available nonpaged pool.
The exact numerical limit will depend on your system, but it is likely to be at least in the order of hundreds if not thousands.
When the pipes are being created using the WCF Named Pipe Binding, you can only create one pipe per base address, due to the way in which this binding publishes metadata about the pipe being used. It is therefore best to define WCF endpoints using absolute URI addresses rather than base address + relative. Provided you do this, and design a reasonable scheme for creating a unique absolute address for each endpoint, there is no fixed limit that I know of to the number of WCF endpoints you can create.
The actual practical limit on any particular system can only be discovered empirically. If your goal is to have a few tens of endpoints, I would guess that you will be able to achieve this comfortably. If you want to have thousands operating concurrently you may bring the practical limit of system resources into play. Only testing will determine this for sure.