The share difficulty submitted will not theoretically make you mine faster or slower although you will see higher variability in displayed hash-rate (since it's calculated based on diff1 shares submitted) with higher difficulty shares.
The payout should* be the same over time if you mine at 16 difficulty or 1024 with that card. Diff1 share just means one share at difficulty 1, and is used to calculate stats for many functions. A share of difficulty is worth 16 diff1 shares, 32 = 32diff1, 1024=1024diff1 etc. On account of that, mining at 16 diff vs 1024 diff for 24 hours should, in theory, generate the same number of diff1 shares, making the payout equal. Of course with good luck, higher difficulty shares can lead to more (or less with bad luck) diff1 shares submitted, but over a long time it should be equal.
*The reason you are getting 50KH/s and many low diff shares, yet getting 90KH/s with high diff shares is because the network is getting flooded (or program, computer, etc) from submitting so many low difficulty shares. It would be smart to watch the pool's website where you mine to see what it reports your mining speed as, and go with the highest hash-rate you can get, as shares submitted are only relevant when taken together with the share difficulty and time mining.
I have several Antminer S1s that hash at ~195GH/s, and if they are trying to mine at a pool that only allows for diff1 shares, all of my miners have significant problems and disconnect frequently, therefore, I set my difficulty high and it has seemed to improve my hash-rate, but simply due to the number of units running and only submitting diff128 shares; now I submit diff1024 and it seems more efficient than before. I also tested this multiple times over 24 hour test periods, but this could vary greatly on your conditions (internet connection, # of miners, pc controlling the miners (rasp pi running a proxy or miners REALLY helps with higher difficulty shares), and other such factors.
One helpful statistic that is shown in CGMiner and BFGMiner (not sure how to make much show on cudaminer..) is the WU, or workers utility, number. This number represents the number of diff1 shares submitted per minute (while the U, or Utility, number tells number of shares per minute at multiplied by current share difficulty). WU is a quick way to check for small improvements in your mining configuration.