Me and a friend of mine where hunting queens. He got the queen down to where it will only take one load of swarms to kill it and told me i could kill this one. i shot it with every thing i had. the swarms and gems hit the queen and it made the beep noise but the queen took no damage... but when my friend shot it, it died right away.

Whats wrong?

Your friend may have mis-estimated how much damage was needed to kill the queen, or perhaps you were lagging.

The queen only shows damage in increments of 5% or 10%.
I've noticed this too.
Maybe even less than 5%

and today i was dueling someone and when i hit him it made the beap noise but he took no damage.. could this be because of lag or what ?

Yes.

I'd guess that the Queens are actually taking damage, but not enough to make the damage indicator in the top right change. The damage to other ships is sent as a 4 bit value, so the target damage indicator bar can be as much as ±3.33% off from how much damage the targetted ship has actually taken. For the Queens & other ships with a lot of armor, that 3.33% can be a fair amount of damage.

http://www.vendetta-online.com/x/msgboard/2/9817#112424

In my experience, the graphics may appear to be hitting my target, but due to lag may not actually register as causing damage; but if I get the audio beep indicating a hit, it has always registered as causing damage.