“The flash drive is now NTFS, I suspect I did that for trasferring big files over 4 gb.”
The only valid reason for doing so IMO.
“I don’t know what I miss out for not having those apps I deleted”
The app most likely is SanDisk’s SecureAccess app. It can be downloaded and copied to the USB drive if you want to restore it. It is good for securing files you want to limit access to. It is not good for securing everything. It will not make your USB drive faster.
“I mostly worry about the files trasnfer speed”
Things that will make your USB drive faster:
FAT32 - less overhead
USB ports 2.x or 3.x
Setting Windows’ Removal Policy for the drive to Better Performance. Requires ALWAYS using Windows’ Safely Remove function when removing the drive.
Buying a more expensive model.