NIOS2 HW & DIV Instructions + FPU

The sine/cosine implementations of the IEEE variant of newlib use lookup tables to compute the result so I wouldn't expect adding the FPU to make any difference at all. If you want a faster implementation you either need to look for software optimizations or implement the sine/cosine in hardware and bolt it up to the CPU as a custom instruction. There are compiler flags you can pass in to tell the tools to use the custom instruction implementation instead of the software library.

Optimizations you can look at are taylor series, cordic, etc..... Some may work well in software with the FPU and some would make more sense being offloaded into hardware. There are others you can look at if you want to trade off accuracy or have inputs that are bound to the point where you can use lookup tables efficiently.

If you are seeing those 'custom' opcodes without a custom instruction then I would think you are having the wrong code linked in. It could be that code is being linked in but never executed but that would surprise me.