Normis, reasons why USB Flash much better.
Flash)Most is -10 to +60, Extended: -40°C to +85°C
HDD)Maximum operating temperature change even is limited, and operating range 0-60C
Size of solution. Especially for Mikrotik - HDD not suitable at all, as i know modern HDD's not less than 40Gb. More space - completely useless, and you are paying for it.
Price. 80GB hdd beginning at $30, USB flash begins from $10-$5. When you deploy about 200 PPPoE's, and you save $20, it is $4000, you can invest them in something really important, than useless space.
Power requirements, maximum start current, DC about 2.8 amps, and in idle mode 8watt. While flash on write (it is peak), about 40mA. Serious reason, if you run Via CPU based low-power router, with DC-DC power supply.
Compatibility, USB stick can be plugged in any PC, and cable let to put it any hole in PC, if you need to hide it. It doesnt have limitation to angle of mount, doesn't require tight screwing to case.
Hotplug. Anybody will say - why for router? Easy - if you want to migrate to another router, you can unplug USB, while old is running, run new router from IT, and then just by one click enable/disable ports on switch, if you dont have stateless apllications and it is just router - it will run without stopping.
Availability. USB stick you can buy in any supermarket, HDD usually sold only in PC shops.
And most important reliability. Read cycles as i know almost unlimited, sure it has MTBF, but most weak point write cycles, which is not a problem for router. HDD in opposite have moving parts, and finally you will have issues with head positioning system or spindel motor, it is moving permanently, and if you will try to save it by putting sleeping mode - you will face limitation of start-stop count.
Speed. USB 2.0 Flash able to archieve 27MB/s, with truly random access, with harddrive speed on (bad scenario for HDD - random access, usually it is router boot) - 16Mb/s.
CF is not an option, it is just rare. Many of Mikrotik customers living in poor countries, with weak infrastructure, especially Middle East and African countries, and to find or ship CF solution - it is expensive and difficult question. And biggest problem not CF, it is available in shops for digital cameras and etc, the problem is CF-IDE converter. And by the way, while camera manufactures slowly moving out from CF, it is becoming more rare in shops. While USB sticks available everywhere, and last SD card what i buy for my wife(for digital camera), you can turn by another side, it has USB connector, and it will appear as USB stick. And size is extremely tiny, everybody know what is the size of SD card.