Since the PSoC execultes compiled code, Ideally the speed of Emulated_EEPROM memory access doesn't depends on the amount it occupies the Flash. We need the following information to help you better:
1. What is the size of Emulated_EEPROM you are using?
2. We would like to see the firmware flow of your project and test the speed at our side. Can you please attach your project? Please let us know how are you measuring the speed of the Em_EEPROM read.
3. Are you using custom board? If yes, can you please attach the schematic of your board?
Thank you. Indeed I also would never expect this behavior... The size is 90112 bytes (together with the code it consumes about 83% of available flash on uC). Everything is being done in the CY8CKIT-059. The speed drop is noticeable just through the UART print of the structure : If all zeroes the screen rolls very fast, if a large part of eeprom is filled it is very slow. As for the code, it relies on many sensors in order to run, so it's a bit convoluted for you to bypass the algorithm and test without the sensors in place. I will try to send you as well a stripped version of it only with the writing/reading/printing part.
I am eager to know the status of this problem you observed. Any new observations?