It is probably a good thing that Yamamoto was transfered so soon after leaving port, within 10 days. That way not too much stuff has been moved around and Hirata can train a replacement if they really need one.
Or that will be a constant hole in the department until Ryuske Domon (Jason Jetter) arrives some years later.
One department that didn't seem to get replacements until the third series was the Life Sciences Division. The Science department got a few new people here and there, but not in numbers. Most replacements seem to be Engineering, Combat Teams/Gunnery, Navigation, and the Fighter Squadrons. Though to be fair, it was rare to see the Life Sciences Division taking casualties since they are probably in the most protected depths of the ship...and not near the generally vital areas that keep getting attacked.