If your code is short and simple, it's best to use the standard plain-vanilla ECHO PHP function.
After studying more about output and output_raw function (found in qa-theme-base.php), they are not simple as their names suggest.
output function is not an independent function, it requires another function called output_array. This output_array function removes /> at the end of HTML tags if any, then check if you choose Minify HTML options or not, and then does some string manipulation tasks.
Even output_raw also does string manipulation.
So, again if your code is simple and neat, better avoid those build-in functions, they just make CPU busier with those extra steps.
If your code is lengthy and non-standard, it is advisable to use them. There are also several online tools to minify codes, so if you use them, you can use the basic echo function for brevity.