Compiling SWI-Prolog with UUID support requires OSSP-uuid library to be installed. It does not work with libuuid as the configure script might indicate. This can take some time to debug as it seems that both libraries are supported while only OSSP-uuid is.
If you have neither installed or only libuuid installed, configure says:
checking for uuid_create in -lossp-uuid... no checking for uuid_create in -luuid... no WARNING: Cannot find libossp-uuid or libuuid -- dropping uuid.pl
This indicates that libuuid might be useful. However, closer examination of the binding source code in the SWI's clib package reveals that libuuid is not supported at all. There is no uuid_create function in libuuid.
For now, it's easiest to just install OSSP-uuid library and make sure that the configure script picks it up.