Looks like I've figured out what is the issue with Nanopool, it is their 120k diff. value. With my 4k hashes I've got 80 ETNs in 12 hrs, while using 80k diff. value on space pool I would have got around 120-150 ETNs. To complete an experiment I have tried to mine on space pool today with 120k diff. value and got pretty much the same results as on Nanopool. So looks like diff. rating that suits your rig is the key here.
How do you arrange diff in your miner?
It is up to the pool, not the mining app. At space pool you just add your desired diff level after your wallet: your_wallet.your_desired_diff