Androids pop mail is not like Blackberry unfortunately. It's hit or miss for me, but for the most part I get 90% of my hotmail emails. There are options where you can choose to "delete off server" under your options in your pop email screen. You can also choose how many days you want it to sync to.
If you want more reliable hotmail go to your gmail account and add your hotmail to it. Go to Settings/Forwarding and POP IMAP and set it up.
I'm sure there might be other apps out there that will do what you are looking for, but I don't know of any off hand.