If I was you I'd rather focus on keeping your site as user friendly as possible than trying to find out how much hundreds of internal links are or aren't harming your site's SEO. You said the site is doing fairly well, so I assume you haven't had major problems with rankings etc.
I think it's very positive that you keep listening to your customers, instead of ignoring them to change something of which you don't even know the effect. In the end it's better to have 100 visitors with 10% conversion, than 150 with 5%.
What you could test though is placing a larger version of your search bar on a more prominent place on your homepage. Especially a properly working search bar with auto-complete could help finding pages that are now hidden somewhere in your top menu. At first you just place this search bar in addition to the existing navigation. When your web analytics after a while show that many of your visitors use the search bar to navigate through your site, you might want to reconsider removing some of the links in your existing navigation.
About the samples page: I would split it up into separate pages for each category. This will bring the number of internal links down dramatically and makes it easier to find the sample you're looking for. Now the page is extremely long and it's difficult to find the right category. By using separate pages you can also create nice (keyword containing?) url's like /samples/carlton-brick-panels/.
Best of luck!