The Department of Defense Design Criteria Standard - Human Engineering (MIL-STD 1472) Section 184.108.40.206.4.1 Warning Signals recommend a flash rate between 3 and 5 Hz for warnings, so 3 Hz is certainly acceptable. I’m guessing the 3-to-5 range isintended to optimize the light’s attention-getting ability, not count-ability. MIL-STD 1472 doesn’t discuss coding information in the number of blinks (neither do any of the other human factors standards I have).
Section 220.127.116.11.5 Flash Coding suggests you can use a second flash rate to code information, with second rate being as low as 0.8 Hz, which tells me it’s acceptable to go that low if you have to. (I don’t think you want to use a second flash rate in your application since presumably users are unlikely to ever need to use this display. Unless the users have seen both flash rates before, how do they know the one they’re seeing is the slow or fast one? However, different patterns of flashes, like in Andre’s answer, may be worth exploring)
I think instantly perceiving more than three of anything gets difficult. The user has to mentally count the items. That implies your flash rate should be no faster than a person can comfortably count –about 2 Hz, I’d say, which fits nicely between 3 and 0.8 Hz.
This is not a display a user is going to able to read quickly no matter what you do. Even if users could count faster, they’ll probably have to look up the code to know what it means. If fast response is critical, then you’re going to have to redesign the hardware to include a better display.
MIL-STD 1472 recommends a 50% duty cycle.