Can a Shimano BR-M965 caliper be replaced with a newer one? I run my little bike repair shop and a customer came to me with a bicycle with Shimano's Dual Control setup:
http://www.cambriabike.com/StM966-BRM965-PreBled-Hydrlc-Disc-Brake-Kit-XTR-Grey-Fr-750mm.asp

Braking was extremely poor, and although we couldn't see oil escaping, I was eventually able to confirm that both calipers are letting oil go around the pistons.

The levers themselves show no problems.

He would like to replace only the calipers, if possible, because he likes the Dual-Control levers.

I'm thinking about two possible issues:
- Connecting the line: is that the same connection since that time?
- Oil flow: Does, like with the short and long cable pull "standards", the amount of oil pushed from the lever and the pushed surface in the caliper have different combination or does it simply not matter from a fluid's mechanic perspective?

Thank you.
The short answer is no, the Dual Control levers are not compatible with current calipers. 

Long answer: 

Both reasons you mention are valid. 

The master cylinder piston on a brake lever is sized very specifically for the caliper cylinder size, the type of hose, and the reservoir size. 

In addition, the hose fittings are pretty specific to year and model. They may work, they may seal short term, or they may not hold at all. 

Last, Shimano will not warrant brakes used with different combinations than designed. Which means that if you choose to mix and match a brake setup for a customer, the liability is on you. 

If their brakes fail, you are in a world of hurt. 

Great question, though. :)