I think it would improve the user experience if applications that need to be closed were cleaned up before the recycle bin (if selected) is cleaned. Currently, the recycle bin is cleaned first, making it impossible to restart closed applications, leading to unproductive waiting time for the user.
There should only be files that you have deleted in the bin, so unless you have deleted something that you shouldn't have then clearing the bin has no effect at all on how apps open.
If an app is slower to open after you have run CCleaner then it is the cleaning of that app's own cached files that is causing it, not the bin at all.
For example if you clear the Adobe Reader (or Adobe Reader DC) files then Reader will be slower to launch next time you open it - because it has to reload the font files etc. into the cache again.