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.
In addition to what was described by fusion, there's something else to consider. In the above example, both drives were the exact same speed, you'd think there was no difference.
However, while your system is ripping data off the HD, it is at the same time writing data to temp files and swap file. If it's reading the data for your programs off the same drive as it's writing to, it has to alternate between one action and the other ... read then write .... read then write.
If they are separate drives, then the two drives can act independently. With samll programs, you'd never notice the difference.... with large programs and files, it's quite significant.