I find out that departments count only the publications published in journals of their own discipline. This is true both in the acceptance decision and in the tenure decision.
While it's certainly possible that some departments would adopt a foolish policy of this sort, which is effectively tantamount to a decision not to have any interdisciplinary researchers, I think it's also possible that you are misunderstanding what the statement that "departments count only the publications published in journals of their own discipline" means. When interpreted in the right way, this statement may be a lot less troubling than you might think.
Specifically, the way promotion decisions typically work for researchers who have a joint appointment in two departments is that each of the departments does its own review of the researcher's work, and the input from both departments is then reviewed by a higher campus committee and taken into account to reach a final decision. Moreover, each of the departments doing the review knows full well that it has only partial "ownership" of the candidate's time. So, to take an example that I am familiar with, a researcher who has a 50% partial appointment in a math department and a 50% partial appointment in a biology department will have published some mixture of math papers, biology papers, and papers that are about both math and biology. Now, it is true that in its review, the math department will "count only the publications published in journals of its own discipline", in the sense that the math department doesn't have the expertise to evaluate work in disciplines other than math and will only be seriously looking at the math papers. But the math department also knows that the researcher only has a 50% appointment in math, so all its expectations regarding the amount of math research the researcher should have produced will be weighted accordingly. The biology department will apply similar reasoning. The end result would be that if the researcher is overall as productive as a typical single-discipline researcher, the promotion review will have a successful outcome. (In fact, because of the existence of papers that can be appreciated by both departments, there can even be some amount of double-counting that may lead each of the departments to conclude that you are producing more research than they were expecting you to produce -- this will probably be a weak effect, but note that it will work in your favor rather than against you!)
I would encourage you to ask at any department where you are considering applying for a job whether the above interpretation of the promotion process is a faithful description of their approach to evaluating the work of interdisciplinary researchers like yourself.
With that being said, I should add that from my observations I find it very true that interdisciplinary researchers have to work a little bit harder than everyone else. Being a member of two departments is a big headache: you have twice as many colleagues to get to know and to get along with; twice as many administrative processes to get used to, department-wide emails to receive and respond to, etc.; and, most importantly, when you come up for promotion you need to find a way to effectively communicate your research to two groups of people with very different backgrounds and research cultures. Perhaps there will indeed be times when you feel you need to work twice as hard as everyone else, but as a general rule saying that you need to work twice as hard all the time is a wild exaggeration -- as others have noted, this is both physically impossible and a highly illogical expectation, considering the fact that I strongly doubt you are paid twice as much as other researchers.
Finally, on the positive side, you should remember that working in two disciplines can often also be twice as much fun!