steorn,
As far as I know, the individual functions must be wrapped in order to use the native interface. For instance, I've seen C++ code which wraps other C functions (from DLLs, for example) as a JNIEXPORT function. You can then import these functions into Java. Wikipedia actually has a
great tutorial on how to do this. If your company is going to be using DAQmx a lot, it would be wise to write a wrapper for all (or at least the most common) DAQmx functions. A quick and dirty solution would be to write the DAQ part of your application in a single C++ function using the DAQmx C API. Then, from your Java code you could call this function to get your data.
Hope this helps,
Ryan Verret
Product Marketing Engineer
Signal Generators
National Instruments