Does RTC have issues with a very large number fo files?

I use the Eclipse client, and usually load about 30K-60K files in my sandbox ... it takes a while to download all the files initially from the repository to my local disk, but after that an "update" is instantaneous ... the RTC eclipse plug-in uses Eclipse editor notifications to notice when I've changed files, and the server protocol for what has changed on the server is proportional to the number of files that have changed, and not to the size of the workspace.  And even when I say "refresh" (in case I've modified a file using some external editor), the "refresh" is just a minute or two.   So you should be fine. 

you will have similar problems. in my prior job, the company had remote builds from central RTC storage.
basically consumed our entire network bandwidth.

distr SCM is not easy to manage, it requires a complete RTC complex install in the remote location too.
and double license usage during cross repository synch operations.

see my design to mitigate this problem here
https://jazz.net/forum/questions/112889/caching-server-useful-for-rtc-workitems

RTC will be able to handle your situation. Based on what you have mentioned, you should organize your files into components and keeping the size of components as small as possible. A component is a collection of logically related files/directories. You can create streams by adding components to it. For a remote access situations, you could use distributed scm. You can find more information here - https://jazz.net/library/article/535/