Would putting only one counter on Ratchet Bomb, then using the 2nd ability kill a Misscutter Hydra?
Yes.
1/1/2011 If the mana cost of a permanent includes {X}, X is considered to be 0.
{Ratchet Bomb}
{Mistcutter Hydra}
Can also be used to kill tokens.
1/1/2011 If Ratchet Bomb's second ability is activated while it has no charge counters on it, it will destroy each nonland permanent with converted mana cost 0.
1/1/2011 If a nonland permanent has no mana symbols in its upper right corner (because it's a token that's not copying something else, for example), its converted mana cost is 0.
Ah {ratchet bomb} you made me so sad when it didn't kill an animated {inkmoth nexus}
As a side note I think I found the perfect card to link for those, can I do this with a thing that just entered. Look at that ruling text on inkmoth that's pretty nice