As Ignacio mentioned, using ISP does not require a bootloader, however, it is also very nearly mutually exclusive with retaining one.
Does programming via ISP clear the bootload, if installed previously in the chip?
Indeed, it does. The ISP interface on the ATmega cannot erase individual pages but only the entire chip. This is distinct from the SPM instruction used by a bootloader running on the chip itself, which can perform a partial erase. It is also distinct from the ATxmega, which does apparently offer an ISP page erase capability.
So in order to end up with both a bootloader and sketch on the ATmega, you would need to erase the full chip, and then load both the bootloader and the sketch, either in a unified hex file or by loading one and then the other to distinct already-blank memory regions while using the -D option to tell avrdude not to perform an automatic erase.
I do not believe the the Arduino IDE supports this, rather its menu option to program a sketch via a programmer is intended to set up a chip for operation with a sketch alone and no bootloader. There does not appear to be any way at GUI-level to configure it to do otherwise.
Someone determined enough could probably craft a customized board configuration that built a functional bootloader into every sketch (or merged or additionally programmed a pre-built one), allowing one shot installation of both an operable sketch and an operable bootloader that could field upgrade it. However, the Arduino IDE would be a poor choice for production programming...