How do I Detect/Defend Against an throw in In Bridge?
Unfortunately, the literature seems to be lacking regarding this (unlike squeezes!).

The key to any good defense is counting, trying to figure out what is going on and what is likely to happen.

There might be some indications that declarer might be going for an endplay. As you noted, one of them is when declarer is ruffing out side suits. This is actually one of the most common ways for an endplay in suit contracts (and even has its own name, I believe: Strip and EndPlay).

Sometimes your own hand will make you alert to the possibility of an endplay, for instance, you hold AQ of a side suit over declarer and declarer probably holds the K etc.

A count of declarer's/defense's tricks, and an idea of how he might try and obtain them might give you another clue as to whether an endplay etc might be coming. 

The best way would be to get familiar with the hands which might have an endplay, and that can be done by playing (with good players) and reading. 

For reading, I would recommend Killing Defense at Bridge I,II by Kelsey.

Not sure if it helped answer your question.