There is no reason to follow the advice to keep a low number of links per page. Here is a visualization of the number of links on the homepages of top 98 webpages. Very few have less than 100, and many have 500 or more. If the top websites don't limit the number of links, then you don't have to either. Google's "100 links per page" advice is very old. The web has changed a lot since they started saying that in 1999. From an SEO standpoint, having lots of links on every page can really help instead of hurt, especially if those links are usable.
Edit: Google removed the "100 links per page" from the webmaster guidelines some time ago. Matt Cutts just released a video where he says that the limits for page size and number of links per page are much higher than they used to be.
On the flip side, the biggest downside of a multi-level menu is that it pushes the majority of your Pagerank to the pages that are in the menu. Since those pages are linked on every page, pages that aren't in the menu can have a hard time competing. If your menu covers all your important pages, then there is little reason to change anything. But if you have important pages that aren't in your main menu and you are having trouble ranking then you might want to consider revamping your main menu.