A carburetor is a carburetor: it doesn't matter what kind it is - it allows air to flow through it and meters the fuel to produce the optimal air/fuel ratio to allow the engine to run.
That said, you'll have two things to look at:
First, fitment. Will a different carburetor physically fit within the confines of the current carb? Will the carb output size match up with the intake on the cylinder? Can you adapt the throttle cable to run the new carb? You'll have to ensure the draft is the same (side-draft carb replaced with a side-draft carb, etc). You could put a down draft carb in place of a side-draft, but it would necessitate some unwanted plumbing, pure ugliness at the carb location, as well as a probable loss of performance.
Second, capacity. Is the CFM (cubic feet per minute) rating of the new carb approximately the same as the old carb? Is the new carb going to provide the right amount of fuel for your engine? If not exactly the same, can the new carb be adjusted (through jetting changes) to provide the right amount? Remember, a 1000cc engine from 1978 is not going to have the same fuel needs that today's 1000cc engine will have. Motorcycle technology has come a long way since 78, that's for sure.
As for a direct replacement, I see advertised the Keihin pn# CR29-GS10-E as a direct replacement. It is ~$2-300 less than the Mikuni carbs on the same site. I was also able to find rebuild kits at this website, which seems to be much cheaper than just buying different carbs.