Before I address the “drop shadow” question, I will say that I personally wouldn't create one large file for all the smaller images. Every image/product should be it's own file with it's own unique files name (preferable the product/part #). It allows to identify each product not only in your InDesign document but also in your files structure. I sort of equate it to doing a 500pg. catalog as one big ID file. That's putting your eggs in one basket and if something God forbid goes wrong, it can be costly. Plus, you avoid images shifting within the frame and products not displaying correctly within your picture box. Yes, it might be easier doing it your way but in the end you might set yourself up for frustration in the event that one of those large files containing all the small images becomes corrupt. Of-course, that's just me and I'm pretty anal about file structure and organization. Don't know if that's good or bad? LOL!
As far as drop shadows go, InDesign does a great job with drop shadows and I don't see anything wrong with it BUT I would always advise to create your drop shadows in Photoshop. Heck, I would even suggest rotating any images that need rotating in PS instead of within ID. Do I follow my own advice, well, no. LOL! I do most of the time but occasionally I do use the drop shadow feature within ID and haven't had a problem with to date. I'm speaking from more of an old school mentality and many of these rules become non-issues as the technology improves and all these applications start to meld into each other. The Adobe CS suites is a perfect example of it all coming together.
Hope this helps!
~erick