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A mix between both sounds good.

Just play Dota 2.

Maybe two different modes or difficulties? On easy you have those rules to learn how everything works out, and on hard, once you've learned the basics, you have the freedom to do it however you want to.

Ever played Tropico? Like that.

Depends on how the rest of the game works, really, and which would fit better. But they're both good mechanics.

I think a predetermined number of slots for each job would be best. Like a Level 1 science facility could host up to 30 scientists, 5 maintenance workers and 5 security guards. You could upgrade it to Level 2 to increase those numbers and the science output. Of course, it could also work with less than the max.

What about fixed number of slots (ex. 4) and fixed type of jobs, but you can choose how to fill them?

I.E.
4 slots, Security & Maintenance ==> 4 security OR 3 security, 1 maintenance OR 2/2 or ...

B seems pretty nice as, well, it has more organization and it could provide bonuses to stuff based on percentages (60% are scientists, for example) while A just seems fixed and would give fixed bonuses.

P.S. Ignore the example, my point is B is for better.

As someone said above, 2 different game modes sounds good.

I prefer B.
I'm pretty interested in the game.
Is it still in development?

A little lost in here. you might want to give me some context ,.

I'm very fond when it comes to mechanics or methodology of a game.

As matthewoods proposes, basically your option a, but instead of just filling out all slots, having a total number of slots inferior to the per speciality slot available. total 20 slots for a 10 science, 8 tech and 5 security for one facilty.

Do you want help for designing it? I know quite a bit about UX and can lend a hand. I have site just for that, also.

Well, were you planning on KISSing your game? If not maybe you could have slots, but have certain numbers you could assign to the cards/jobs you would put there which would affect more of what said card/job's ability. Or maybe like... Modifiers on weapons on some games? While one may have say... Accuracy +11.74 and Damage +30.00, while another might just have full on Damage +60 or something... Slots for cards that change things even more, mixing elements of the various jobs.
I do also like snowleopard1024's idea.

Of your two options however I would go with (A) I do enjoy having something simple and organized.

Depending on how hard the task is, it should require a number of people that can handle the given task when they work together.
Example, in the office you only need 1 secretary but ten office workers to maximize output. It would also be nice to go over the maximum output to increase production a little but with diminishing returns as those extra people won't be able to work all the time since the workforce is bigger than the workload. So if you put like 20 workers on a job that only requires 10, output could be like 150% instead of 200% or something. It's up to you though because I don't know what your game is about and it's hard to suggest stuff when I don't know the context.

Or maybe if a job has no workers for a while, work piles up and then you can put like 20 workers on it to get the job done, and once it's done you just leave 10 workers so they can keep doing what needs to be done and the rest of them has no work to do anymore.