Via ftp, I just had a look in /modules/by-module/Bundle. Why do a large number of the modules in there start with the name "Bundle-" but many do not?

A distribution may contain a number of modules that are unrelated to the distribution name. For example, one of the distributions listed in /modules/by-module/Bundle is Apache-ASP; the reason that appears there is that this distribution contains the Bundle::Apache::ASP module.

Incidentally, when I go to search.cpan.org and click that link on the left that says "Bundles (and SDKs)", why don't I get that massive list I see in /modules/by-module/Bundle? Isn't CPAN search trying to show me that list here?

In general, the entries in the categories on the search.cpan.org main page come, in part, from a category selection made by the author at PAUSE when the author registers and subsequently uploads a module. If such a category isn't chosen, it won't appear in the chapterid field of /modules/03modlist.data index file on CPAN, nor when one browses CPAN by category.

Having said that, search.cpan.org adds, in some fashion, distributions to the existing categories that CPAN already has. However, the algorithm used is different than one gets by browsing by module.

If "distributions" are indeed separate and distinct from bundles, where can I go to browse them?

If you go to a distribution on search.cpan.org (for example, see Apache-ASP), follow the Browse link to examine files in the distribution.