The enzymes produced by smoking wouldn't just be localized in the lungs as they would travel the bloodstream and affect other tissues. Smoking's effects on blood vessels (like in arteriosclerosis) will definitely affect the penis either directly or indirectly as the penis is essentially a spongy collection of smooth muscle tissues similar in composition to blood vessels.
There's even a condition known as "penile arteriosclerosis" in which the conditions seem especially localized in the penis.
Here's an excellent article that outlines the many ways in which smoking can affect the penis (please note the extensive references):
Smoking and vascular impotence SAMT DEEL 70 13 SEPTEMBER 1986 329
Hold on your making some jumps here, the previous article you linked to regarding emphysema indicated that the protease inhibitors and the tobacco chemicals were bound site specifically in the lungs ( lungs with injuries caused by smoking ) causing the advanced break down of Elastin. Fair enough, that makes sense.
The article didn't say that new enzymes were produced, just that protease inhibitors were directly interfered with by tobacco chemicals.
Now we know that vascular damage occurs because a similar process as that which is going on in the lungs takes place in the vascular system, tobacco chemical, transmitted through the lungs, in the blood bind with protease inhibitors in the arteries causing degredation of Elastin and eventually arterial sclerosis. Fine this all makes sense.
This naturally can cause problems with erections, since as you say the penus is mostly a sponge of blood vessels.
But this doesn't mean that your penus has actually shrunk, it just means that it's blood vessels aren't capable of carrying enough blood to give you strong enough erections to expand it to its fullest extent.
Now from what I know about arterial sclerosis, it is commonly an inherited disposition, though it can occur with no family history, but as with the evidence produced in the study on emphysema, I was under the impression that arterial sclerosis was due to a lack of proteins and other factors necessary to repair the arteries and keep them in good shape from all the wear and tear they go through. With some inherited types of arterial sclerosis isn't the gene responsible for coding for the production of the requisite proteins switched off thus leaving the carrier unable to produce them leading to progressive arterial hardening and furring and other kinds of damage ?
There's no doubt that smoking would be extremely dangerous to people with this form of the condition.
But my question then becomes, if Elastin is depleted by rampant elastase in smokers blood how come they don't die of multiple organ failure not associated with cancer ? And secondly I thought there was no doubt surrounding the claim that smokers are more inclined to suffer with connective tissue problems like arthritis e.t.c. and that new studies were showing no statistically significant increase of incidence of these conditions in smokers, and that like many things the main predictor of these conditions was genetic ?
If this is the case then surely the interaction between protease inhibitors and tobacco chemicals is far more specific and not generalised to the entire body, and factors like lung damage and genetic tendency to lack production of protease inhibitors would become the deciding factor, and impotence caused by smoking would be evidence of over all arterial problems, no ?