I would think there'd be enzymes in nearly all living cells, including muscle cells and the other connective tissue present in meat (marbled fat, other juices and organic matter present). I haven't been able to find a solid answer though, this is just my common sense guess. I base this guess off the definition of what an enzyme does and the fact that there has to be some sort of chemical reactions in muscle tissue in order to cause a contraction or rebuild muscle tissue:

http://science.howstuffworks.com/dictionary/chemistry-terms/enzymes-info.htm
"Enzymes, complex proteins produced by all living things. They play an important role in nearly all the chemical reactions that take place in organisms by acting as catalysts. (Catalysts are chemical substances that change the rate of a chemical reaction without themselves being changed by the reaction.) Most often, enzymes allow reactions to begin sooner than they would in their absence, thereby speeding up metabolic processes."

As to the mention of proteolytic enzymes, I know still less, but for those who might be trying too understand too here's a link to the definition or my abbreviated interpretation:
An enzyme that helps break down proteins into smaller components.
http://www.britannica.com/EBchecked/topic/479818/proteolytic-enzyme

Based on the definition it seems unlikely for there to be much of this type of enzyme in the muscle tissue itself since it would cause the muscle to break down, but it may be there in a latent state or small amount in order to strip away damaged or old tissue.

I guess the obvious downside for certain products is that this process would kill good bacteria as well, but I suppose they could re-add it after all the bad stuff was killed.

I also wonder if by destroying the bacteria if it's components or nutrients become bioavailable and enhance the nutrition of the product.