No, because all current flashcarts are still running in DS mode. Meaning, none of the upgraded hardware on the DSi are being used.
Also, if you've actually played the retail carts of some games like GTA:CW, it will also lag when there are lots of stuff on screen. Generally if something lags with the retail cart, it will on a flashcart too no matter how fast your microSD is. There are a couple things you can try to minimize it though:
1) Ditch the R4 and get a better card
2) Get a higher class microSD like Class 6.