"More instructions to execute" is not synonymous with "slower".
NaNboxing lets you use less memory on certain use cases. Because memory access is slow and caches are fixed size, this is usually a performance win, even if you have to do a few extra ops on every access.
I mean, a modern computer is operating the gigahertz range. Adding a few extra bitwise instructions might be something like a nanosecond. Which is absolutely fleeting compared to memory operations.
NaNboxing lets you use less memory on certain use cases. Because memory access is slow and caches are fixed size, this is usually a performance win, even if you have to do a few extra ops on every access.