What are the implications of using PROGMEM?
Here is a quick comparison of FLASH, EEPROM and SRAM on the AtMega328, the microcontroller in many of the current Arduino boards (excluding Due, Leonardo, older Arduinos and some other compatible boards).


FLASH: 10,000 write/erase cycles. Access is fast, but slower than SRAM. Code accesses via PROGMEM.
EEPROM: 100,000 write/erase cycles. Access is slooooooow, in milliseconds. Relatively complex access procedure.
SRAM: Unlimited write/erase cycles. Access is very fast, 2 clock cycles. Direct access by code.


So, the key hypothetical negative consequence of using PROGMEM is the 10,000 write cycle limit.
The key negative consequence of using EEPROM is the complexity of code to read/write/copy data.
SRAM, it's just very limited in capacity.