When to use an Arduino bootloader
The basic answer is that some people don't want to buy or make a programmer. They just need a serial port to program the IC using a bootloader. It's cheaper. 

Or sometime you want to be able to upgrade your code on the field without using your expensive programmer. Then a bootloader is fine.

But if you think about the usage of your system and don't find a need for a bootloader, then there is no reason to keep it. It takes flash space for nothing.

The Arduino bootloader is just a bootloader: something that allows the chip to program itself with new data on boot. Nothing else. Thus having it or not doesn't impact your code performance (except for the available flash space or start-up delay).

Thus answering your question:


If you don't have a programmer -> keep the bootlaoder
If you have a programmer -> up to you, it depends if you want to be able to upgrade without the programmer or not.