Mσᶎ' comment has dealt with the technical reasons quite eloquently, and I'd guess Mσᶎ' analysis is likely correct.
However, I suggest that we can dig a little deeper to guess why the process hasn't been fixed.
Disclaimer: the following is pure speculation. I don't work for TLG (I wish!) and have no special knowledge or insight into the company or its policies.
A Revealing Question
In my mind, the important question is why the instructions are published as PDFs at all? Whilst LEGO is a passion for the fans, it is also a business. The PDF instructions are provided as a free service to TLG customers: they receive no direct financial benefit from the publication of their instruction books.
So, why do they bother? Presumably for indirect business benefits. Things like:
- The hope that customers will buy bricks / sets to make up sets they don't own
- Easier to deal with customer enquiries regarding lost instructions
- Customer good will
Costs and Benefits
Assuming this is the case, we can speculate that TLG have not invested in better PDF instructions because they don't consider the additional benefits will be covered by the cost of improving the quality.
- Do many people really purchase bricks based on these instructions? I doubt it.
- The poor quality PDF instructions are probably good enough for customer enquiry purposes, or at least TLG may perceive that it is.
- TLG may perceive that customers in general don't care about the instructions quality - the few of us who do may not provide sufficient incentive to improve things.
The bottom line is that these instructions are provided on a goodwill basis. Unless TLG receive incentive to improve them, they probably won't.
A Call to Action
So, if you really care about the instructions, what can you do?
I suggest that it might be worth contacting TLG's customer services. If they get enough complaints, they may consider making improvements. Alternatively, they may consider it worthwhile providing a paid service for obtaining better quality copies of instructions.