Andy,
NavData.db3 is the main aircraft, registration, operator and route database that is autopopulated by RadarBox as you pick aircraft up. This is the database that allows RB to show aircraft details. When you deleted it, you would have ended up only Mode S and other details actually transmitted by the aircraft. NavData.db3 fills in all the blanks - so you need this file.
My Navdat.db3 file is only 18,688kb, and I've been using RB for over 12 months now, so I don't see how yours is so big after such a short time.
MyLog.db3 is the log of all the aircraft you have received live via your antenna, and mine is over 54,000kb in size and this contains 2 years worth od data as I imported all my SBS-1 aircraft as well. However, the size of MyLog.db3 does not affect the speed of the program.
Regarding the speed of your RB installation, are you running RB with an Internet connection? You PC should easily be able to run RB.