The bounties she gets only last so long. During times of peace, there isn't a lot of work for a bounty hunter.
Hence, she has to sell most of her powerups to live. Whatever she's got left often ends up getting stolen... or broken... or something.
Except for th energy tanks. She keeps those, but the strength of the enemies keeps incresing exponentially, so instead of having a thousand energy tanks which you lose twenty-to-a-hit, they just scale 'em down each time.
So, why does Samus find it necessary to blow up every place she visits?
Go Moon!