Board assembly costs...

I am designing a product which calls for two capacitors with quite specific relationships to each other. I'm wondering whether to pay more for two tantalum SMD caps, or use one cheap ceramic chip and one through hole cap. The additional cost of the tantalum caps is around $1.00 to $1.50.

The question I cannot answer myself is how much would it cost to put the one through hole cap on? Would it be cheaper to just go with the more expensive tantalum caps so I can stay completely SMD? I just don't know how much the additional assembly process would cost.

And experiences?

That's a question you really have to ask the company that makes your boards, as it depends on their process capabilities and what they would have to change to allow the through-hole component. If your board is already is drilled the two extra holes won't make a difference however it's up to their pick and place machine (or personnel) being able to do the throughole components at the same time as SMD, could be nothing could be expensive depends completely on the board assemblers capabilities.

I would have thought that the cost of manually fitting a capacitor would be far less than $1, unless the process of making the boards right though to packaging the finished item is completely automated.

If they are the same part, go for the same part. The less "reels" the better.

EXPECT to pay an extra $0.50 for every hand placement at 1000pc production rates. ceramics can be lower values in some applications

I'm guessing the other cap you're putting with the ceramic one is an electrolytic? For longevity the tantalums would probably offer better performance.