I'm searching for the complete HEX file for the Atmega 16U2 which is used for the USB Com on the Uno R3.
The original File is located in the Arduino install files.
As you point out, it is in the Arduino install files. You can search for it with the Windows search feature, it is called Arduino-COMBINED-dfu-usbserial-atmega16u2-Uno-Rev3.hex. On my computer it is in the C:\Program Files\Arduino\hardware\arduino\avr\firmwares\atmegaxxu2 directory. If you want to modify and re-compile, there is a README.txt file in the same directory with explanation of the bootloader and USB to serial program source files and info about the VID/PID used for each program (bootloader and USB to serial program).
Arduino-COMBINED-dfu-usbserial-atmega16u2-Uno-Rev3.hex is the complete contents of the Uno 16u2. It is 2 programs: the DFU bootloader and the USB to serial program. It has the Arduino VID/PID when it is running the USB to serial program, and it has the Atmel VID/PID when it is running the bootloader (when you put the chip in DFU mode by resetting it).
I'll not have ISP connections on the PCB.
It is probably not a good idea to omit ISP connections for a processor. You will have difficulty re-flashing it if necessary, and if the DFU bootloader is not working.
If all you're going to do is USB to serial, 16u2 is probably not the best choice of chip. There have been posts on the forum explaining the reason Arduino chose it is because they got a good deal from Atmel on a bulk purchase. There are dedicated USB to serial chips which are not programmable, and those are a better choice for solid serial communications that won't fail because the chip "lost" its flash memory.
You may notice the forum has a fairly large number of posts where people had difficulties with their Uno or Mega and the resolution was sometimes re-flashing the 16u2 processor. Sometimes the DFU bootloader remains on the processor and new firmware can be uploaded via DFU, and sometimes the DFU bootloader is messed up and ISP must be used to re-flash the DFU bootloader and USB to serial program together (Arduino-COMBINED-dfu-usbserial-atmega16u2-Uno-Rev3.hex).
If you will be doing fancier stuff than plain USB to serial conversion, maybe 16u2 would be OK. 32u4 may be better because you can easily put the Catarina bootloader on it and use the stock IDE with very little modification to upload a USB-to-serial program as a sketch. 32u4 is a Leonardo. The Catarina bootloader will not interfere with your main processor upload through its Optiboot or other serial bootloader. But then if you go down that road, you have to wonder why not just use the 32u4 by itself and not as an intermediate chip between your computer running the IDE and the main processor (328 or 2560 or something else). In the end, it comes down to what you are building and what is its purpose.