Cleans cached data used by the OSGi framework and Eclipse run time. This is useful if you have new plug-ins you have added to your environment. It helps to troubleshoot startup errors after installation, update, or using a shared configuration.
There shouldn't be any issue in using clean option everytime.
But time taken to launch the RAC UI will be slightly more when compared with launching the RAC without clean option
NX 11.0.1.mp01 | SW 2016 | TcUA 11.2.3