I just came this Monday from that sector and yes you have to go through Indian customs both directions... I didn't see/encounter any difficulties... while going in through the customs, they didn's ask any questions and also going to nepal through Indian customs they didn't ask any questions... the only questoin that i was asked when coming back to US through the Indian immigration was "Tum US mein kya karte ho?" answer was "Main US me ..... karta hoon". Other than that it was a smooth transition. I don't know if you've been to delhi... but I wouldn't recommend staying in any hotels.... there is a visitors lounge outside the departure gate and for Rs. 30 you can get in. It has quite comfortable chairs, A/C, TV's small snacks counter, some shops, PCO.. and etc... if you have further questions... fell free to ask again...