File size in pdf export

Hi community,
I have a question about reduction of file size when exporting to interactive pdf.
I am working with an InDesign (CS6, Win) document with about 70 pages and about 100 links included.
The links consist of Illustrator files with up to 15 layers, which I am using to show some step-by-step instructions.
Because of the layered architecture of the included Illustrator files, the exported pdf becomes quite big (>50MB).
I wonder if InDesign has a way of flattening the figures in the exported pdf, in order to show only visible layers?
When I browse through the exported pdf, I see deeper layers being rendered, which finally are covered with an opaque layer.
Of course I could use Illustrator to flatten each figure and link to separate files, showing the final view of the figure.
Or I could export every view of the figure as png and link to that.
However, with both these methods I lose the advantage of linking to one file and choosing the visible layers for the figure - thereby making it not easier for maintenance, besides creating a lot of work for saving the separate figures.
When exporting from InDesign, I already unchecked the "Create Acrobat Layers", however this does not solve my issue.
I also unsuccessfully tried to reduce the pdf file size using the "Save As Optimized pdf" feature of Adobe Acrobat Pro.
Any ideas?
Thanks in advance!
Chris

There has been some progress with the topic:
As Dave Blatner pointed out, adding transparency to a figure and exporting to pdf using the PDF/X-1a preset will remove all hidden information from the Illustrator vector graphic included.
However, this preset does not support interactivity:
InDesign produces a warning, stating that all interactivity will be lost and one should use PDF 1.5 or higher to support interactivity.
Unfortunately, these PDF versions do not support "Transparency Flattener" anymore - putting me back to start.
But maybe I can form my question a bit more specific now:
How can I drop all information on an exported pdf page that is not visible (while still having interactivity)?
Any hints are gratefully acknowledged.
Chris

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