This would mostly depend on your secondary hard drive. If your primary hard drive is faster then you would be better off installing to your primary drive. However, if your secondary drive is just as fast as your primary, you're not going to run into any issues. However, it's not like you will see a performance increase either.
Your boot time will be mostly dependent on the programs you have starting up with windows as well as what your hard drive specs are. It doesn't matter how fast your hard drive is or what hard drive you install the program to, if you have 20 programs trying to start with windows, it will take longer to boot.
Hope this answers your question.