0.00099 is far above the dust threshold. It is 513 satoshis or thereabouts. The monetary value, even assuming 0 txfee, is much less than one cent.
The current dust limit is 2730 satoshis. It used to be 546 before all the 'stress testing'.
Correct. It depends on relayfee. Now that mempool limiting has been implemented (in 0.12) it is safer to lower relayfee again.