Reapers are also extremely arrogant. The notion someone could tamper with their technology is something they don't consider because they are clearly the superior race. The notion that their plan might fail is also something they don't consider, after all they've done it thousands of times already with the same outcome each time.
A better question about Ilos is how are the ruins in such good condition? After all, these aren't Prothean - they are from a race before the Protheans, the Inusannon. And those ruins are in better condition then Prothean ruins half their age! Obviously very well built!