Of course, the same note from various instruments will each have it's own timbre, which include other frequencies, too. Some bass instruments might be more amenable to localization than others because of these differences in timbre, obviously. The doubter should connect two subs, turn off the main speakers and try various test tones himself. Few, if any musical instruments, emit a pure tone, although I guess synthesizers can, and may be used that way at times.
Two subs is my limit. More than that, I start to get foolish.