There are not any problems or conflicts with doing this.
And in fact you can run multiple copies of RTKLIB on the same node as SNIP is running. This can be of value when you are using the native ability of RTKLIB to translate a vendors propriety GNSS format into the standard RTCM3 format normally found on a NTRIP Caster such as SNIP.
Hint #2: Planning to run multiple copies of RTKLIB on the same machine with different settings?
It is best to have each copy in its own folder with its own binaries. As the Windows GUI in RTKLIB in fact calls the command line program, you can easily create a 2nd copy by clicking on the launcher, and it may run for some time without issues. But both copies will write their ini file to the same place and this can cause problems over time. [The last copy you close will be the only setting that are kept, but temporary orbital data is kept this was as well]
It is best to just clone the entire folder and have separate environments. We often have several preset copies here which we use for testing setups. With each in its own folder, they do not interfere with each other.