Not doing any kind of reconnaissance before a conflict would be crazy! But I guess maybe they didn't think of it!
It's also my working theory of why we won in Independence Day the movie :) Aliens were never warring among themselves and/or allowing any kind of a hacking culture, so didn't think to secure their systems!
I had come to the same conclusion with respect to ID which made the plot a lot easier to swallow.
They were essentially a hive mind working with a single purpose and were therefore incapable of conceiving the notion that they would need to secure their systems against an attack that essentially used their own technology against them.
It's also my working theory of why we won in Independence Day the movie :) Aliens were never warring among themselves and/or allowing any kind of a hacking culture, so didn't think to secure their systems!