You get more shares with Ethermine because they use a lower share difficulty. Lower difficulty = more shares worth less each e.g. 100 shares at diff 4000MH are worth exactly the same percentage of a block as 40 shares at diff 10000MH. Using lower share difficulty for higher hash rates is inefficient because you are getting work and submitting shares more often, increasing the load on the pools stratum which can lead to stale shares.
Based on the fixed 4000MH difficulty Ethermine uses, your miner should be getting 60% more shares on Ethermine to be equal to the amount of shares at a fixed 10000MH diff for Nanopool.
nanopool diff is 5000MH not 10000MH, anyway I see better payout on ethermine.