Links of type URL/something/something.html are bringing weight to inner page, which is then transferred to url/(index.html) by internal links on the web-site.
This is not the same as link to URL/ that brings weight (or PR) directly to main page.
Google treats each page of a web-site separately giving them separate PR.
Depending on which keywords website is targeting it can be decided which kind of links can be more useful.
If website is targeting rare keywords, having separate internal page for each keyword combination, then links of type URL/something/something.html are needed.
When website is targeting something highly competitive like "business loan" than links to URL/ are better.
(imho)