Its Assembly. An assembler is used to translate assembly language statements into the target computer's machine code. Its not technically wrong to call it assembler, but assembler really is something completely different then the language itself. Its confusing =\
The robots would on a basic level use computer binary code. Thats how computers work. Now, their programming, which is something completely different (HTML isn't a programing language!), could be in english, but that makes no sense, because all compilers are simply interpreting words into assembly level statements. You can program in japanese too. Pixel knows almost no english, and he programmed Cave Story, didn't he? I might also add that understanding a language has nothing to do with what language its code was written in. Its code, to the robot, is a bunch of binary commands. You'd have to program it to understand language. How the heck they programmed a robot to have free will without using quantum computing is beyond me, but hey, thats what fiction is for.
Also, haven't you noticed in the readme for Cave Story that "error messages may appear in japanese"? I think the very existance of cave story is enough to demonstrate why something doesn't have to be programmed in english.
Bottom line is, language doesn't matter to a robot, and it definatly doesn't explain why the writing on his hat is in english.