I agree. I'd like to see something like a "pop needed" attribute added to facilities. It might work well expressed as a ratio where 1 is the "average" manpower needed.
Adding up these numbers and dividing the population by the total would give a result showing how over- or under-manned the average facility on the planet is. Bonuses should be applied based on that, not on overall population.
IOW, if you had 3 mining facilities (let's assign them a manpower factor of 1, just for the example's sake), 2 storage facilities (manpower .5, say?), and 1 shipyard (manpower 2?) on a planet, then the total would be 6. If the planet had 600 million people, the bonus would be based on having an average of 100 million people available for working the facility and/or related industries. If the planet had 6 million people, the bonus would be based on having only 1 million workers available.
There might also be a minimum number of people required per facility to keep things operation. I know I could never get anything done with only a million people to help.
I think a production penalty would be a better way to go than shutting down facilities until the minimum people/facility number is reached. Too much bookkeeping involved in the second method!