I understand your position very well because I work in e-commerce too, and many times, the only difference from one product to the next is dimensions. I work with audio visual equipment and this is often the scenario for things like power cords, cables, microphone cables, audio snakes, etc.
If all of your product descriptions are the same, then yes, it's duplicate content. If you are super-concerned about that, then that makes the case for creating hub pages with options that allow people to select the size of the furnace filter they want.
Personally, on large e-commerce sites, I'm not sure that spending tons of time writing elegant, unique descriptions for products that are obviously the same is worth your time. Google understands the difference between a site that is e-commerce based and a site that is content based (like a blog).
I would say, set it up both ways and have some users test it. Which way makes it easier and faster for them to find exactly what they want? Choose that one. I think if you choose the one that is better for usability, the SEO will follow.
Personally, I like hub pages. You know, you could do both. Most E-commerce platforms allow you to build a hub page, and then also have individual product pages that just aren't part of the navigation structure. I have used both Volusion and 3DCart to accomplish this. It just means building all the product pages, creating a "parent" page for your hub page, associating the products with the parent and then just not placing those individual products in any categories. That way, they still get indexed and if someone does search by dimension, it's possible the product page matching their search will be the one they see in the SERPs. That's hard to predict of course, but it would at least make that a possibility.
Also, last thought, if you do a good job of featuring the dimension in your page title and meta description, and also on the page, then I really don't think the duplicate content issue will be a problem.