Why would the Federation monitor Zebes? They've got a lot of space to monitor already. According to what they know, the pirates on Zebes and Mother Brain have been completely wiped out. Think about it; what reason would the pirates have for resettling Zebes? The Federation probably doesn't know they can just clone a new Mother Brain, and they're all dead anyway. There's no metroids on Zebes, there's no Mother Brain on Zebes, and according to what Samus told them there's no survivors left on Zebes.
If I had to guess, after Samus destroyed the pirate base (and flagship) the Federation turned their attention to finding the other Pirate bases and Urtraghus. The patrols like the one in Prime 2 could even be defending the Federation from other threats like the Kriken.
EDIT: Conspiracy theory time! The Ringleaders wanted the Pirate base on Zebes to 'grow back' so that Samus would need to return there. This time, they'd put her through decontamination immediately when she got back and use samples from her suit to clone all of the creatures she fought on Zebes. They'd use cybernetics on the clones and try to 'train' them to create a semi-automated special forces unit that could take over for the Federation police.