It would be nice to have the option to deposit less than 0.001 btc. For example, if I have 2 addresses that have 0.0005 btc each, it would be nice to have the option to combine these amounts without showing directly on the blockchain that they both belong to the same person. (Preferably, this option should allow one to send these two amounts of 0.0005 BTC to two different whirlwind's BTC addresses.)

So, the option to deposit less than 0.001 BTC in a single transaction would be useful even if withdrawals are only possible with fixed values, and the lowest of these values is 0.001 BTC. It becomes even more useful if "fast" withdrawals of non-fixed amounts are possible again, and yet more useful when exchange to monero is available. If such deposits are disabled now because the blockchain fees constitute too much percentage of the deposit amount, I don't see any problems with charging a corresponding fee to such mixes, even if you want to keep the mixes with a single top-up of >= 0.001 BTC fee-free.