Being the intelligent chaps that they are, the Panic engineers decided to look into the cause of this. What did they find? "Will started digging into the files and brother, you won't believe what he found. Swatches, patterns, preview bitmaps, all sort of metadata; even though we'd specifically turned off all the extra options when saving from Illustrator: Preserve Illustrator Editing Capabilities, Embed Page Thumbnails, etc."
Apparently just opening the obese PDFs in Preview and then saving them would shrink the file sizes dramatically. Rather than force their staff to go through this process each time they found a large Illustrator PDF, Panic did what most developers would do and wrote an application to automate the process. Devs can simply take a big batch of files, like the contents of an application's Resources folder, drop 'em onto ShrinkIt (download link), and watch the file sizes magically shrink. According to Panic, ShrinkIt can reduce an app bundle size by 4 megabytes.
While ShrinkIt is a Panic-internal utility, the company has made it available to the world for free. Please note that ShrinkIt is primarily made for shrinking simple vector-resource PDFs, and probably won't work well on press-ready PDFs.