Should I put in a job application email that I am interested in doing a PhD?
Research each company and tailor your applications to each. See what their websites say about training opportunities, and/or reach out on LinkedIn or similar to see if you can informally ask a few questions of friends-of-friends who have worked there.

Situations where it's valuable to mention your eventual Ph.D. goals:


"almost all PhDs are done in tight cooperation with a company" -- talk to PhDs or look at dissertations, and you see that this company has helped with PhDs in this way.
They rely heavily on people with Ph.D.s and it would be hard for you to move up in the company without a Ph.D.


E.g. my old employer mostly recruited undergrads &amp; PhDs, assuming the undergrads would stay 2-5 years before moving on. They were glad they could fit into a trajectory that helps people into grad school (and some return to the company later with that advanced degree). 

Other companies might help fund your doctoral study if you prove to be a worthwhile employee, especially if you can pursue it part time. Or they might give you a loan which they forgive if you go back to work with them afterward. (This is unlikely to happen for you unless the company has a track record of doing this. And if they do, they'll probably mention it proudly.)


Situations where it may be counterproductive to mention your Ph.D. goals:


Few people at the company have a Ph.D. in this field, and most of your coworkers (and bosses) have a Masters degree.
They expect people to stay for a "career", and many people at the company have been there for 10 or 20 years.
It's a fairly small company, so they're unlikely to be able to support your PhD trajectory in the same way a larger company might. 


In general, when you apply you want to maximize the ways that you will fit with the company and not make them worry that there is a mismatch. A company that expects you to choose a different company may be less likely to offer you a job in the first place. But you want to have as many options as possible and make a choice between them.