My question is, bestshare in antminer shows sometimes less than Node difficulty. What does this mean? If its less than actuall difficulty does that mean miner is submitting lower difficulty shares and are discarded by pool because of lower difficulty? Which simply means such shares gives no payout at all?
Essentially yes, your miner will submit shares that meet the pseudo share difficulty, this number is typically much lower then actual share difficulty.
By doing this P2Pool is able to more accurately estimate your hashrate, and present you with better data on the front end.
If you were to only submit shares that meet the minimum P2Pool difficulty it would make the data presented to you on the front end far less reliable because of the time between your valid shares.
I'd be cautious about trusting "best share" on Ants, there have been errors in the past.
I am also thinking even if the Ant shows a "Best Share" large enough to get a share but you don't see it show up in your miners info on a pool, then most likely it was either a orphan or dead? I have only been mining on p2pool for less than a week and have tried a couple nodes near me (Chicago area). I also started off using a couple of wallets on my S3's and S5's so I could see just which pools and/or miners were receiving shares. Now I have consolidated all miners to one node and one wallet. Still learning here but like what I see so far.