IMO, If your original recording is at a reasonably good volume, say minus 10 db or higher, then that is likely a good level for de-crackle, de-click FX to work. But if the original recording is really low dB-wise, then increasing gain could well be an advantage to enable de-clicking and de-crackling FX to work more effectively. The best way to find out is to experiment with this yourself to draw your own conclusions given your audio media.
I usually apply a conservative amount noise reduction on the original file with the legacy NR-2 suite or iZ's RX. A secondary process run can be applied to the events if more is desired. Scanning new noise prints of coarse.