I'd imagine in some cases they'd expect you to be a total idiot that they only bring on b/c they're getting pressure from above (to further what 10:41 said.)

It shouldn't affect your security clearance at all unless you went to North Korea for some experimental treatment.

If it's something that isn't apparent on first sight but will be obvious if you've been on the job for a couple weeks, then why not disclose it?

Federal manager here that has hired 3 Schedule A applicants. Its really about the culture of the workforce and not the certification that you are hired off. There are a few serious downsides to the Schedule A certifications. If you do make a Schedule A certification, the hiring manager has to interview each applicant on the list. This can be very time consuming if you have a cert. with 25 Schedule A applicants.

Personally, I would apply with my Schedule A certification, and without. I have seen this done and have one employee on staff that made all the certs. for the job. This tells me as a manager that the disability might not be visible. Once you start, you can apply for a reasonable accommodation through the RA office to accommodate your office visits. This is really not a big issue, especially if you just need doctors visits and a set schedule.

I would be more concerned if you had a disability that would affect your work performance like mental health issues. I do have two people on staff, one Schedule A and one not Schedule A, with mental health issues.

To me, the most important thing is to find a manager that will advocate on your behalf. From my experience, it is very hard to do this because you face criticism from fellow managers as well as subordinate staff.