When debugging embedded systems, logic analyzers display timing diagrams, hex or in the good ones asm code. Sometimes you need to check your hex file for errors. Sometimes you need to create delays based on how may machines cycles an instruction takes. My point is you can't be a good programmer using those chips with out knowing the instruction set and those programmers can't keep asm in the back of their minds like desktop programmers can.

When writing a program, the question is still should/can the program be coded in a language other than the processor's native one, though the answer is usually yes. Even so, the programmer still thinks about what the uC is doing at the machine level. It makes no odds if 3/4 of your micro program is going to be C expressions like port1 = 0; as opposed to assembly lines
like mov port1, 0. It doesn't matter if you're a student blinking leds or a hired programmer writing a program to control the led display in your microwave.