Hi Johan,
If they are new, the nib and feed would only need some rinsing and flushing with a soapy solution. If they are eye-droppers, that may be a bit difficult of course, you'll need one of those blower bulbs to do it (maybe cut off a piece, so they fit tightly into the section, in order to do this).
Anyway, the problem with ebonite and water really occurs after oxidation has occurred, which one would normally not expect to happen in a few days or weeks or months, not noticeably so, in anyway. So letting it soak for a few hours should be fine. If you see that it actually starts turning lighter, you'd better stop the process.
OTOH, feeds are exposed to fluids consisting of > 99.5 % water anyway, so those shoudl be fine. I would be worried about the whole pen, rather than the feed. I wouldn't like an ebonite pen to soak in water for a prolonged period of time. Whenver I clean an ebonite pen, I do that with a damp cloth, and dry it immediately afterwards, and maybe use some wax afterwards, to protect it from oxidation.
Oh, whether you use water or an ammonia solution, it is still mostly water...
HTH, warm regards, Wim