In regards to the GP38s, the switch from S3L to K5LA was begun while MEC was still an independent company, in the late '70s. The practice did carry over into the first two or three years of the Guilford era, but eventually the practice ended -- due to cost, I'm sure. A brand new K5LA costs a lot more than simply cleaning and rebuilding an S3L. The other factor is that Guilford scrapped a lot of locomotives in those days, which meant that they had dozens of surplus horns available. This is why some of the U18Bs ended up with P5s (taken from scrapped U25Bs).
Even today, horns get swapped out quite frequently, but the company does not make any effort to standardize on one type of horn, or even one family of horns. As long as it makes noise, that's all they're concerned with.
A few examples of recent horn swap-outs:
One of the old GP9s is now sporting a K3L, taken from one of the GP40-2Ws that was in the deadline.
One of the recently-painted GP40s had its original S3L replaced with a low profile P5, which probably came from one of the SD45s.
621 is currently sporting an RS5T. Not sure where that came from, but I'm fairly certain it's not an original Santa Fe horn.
252 had a nice K5LA a few years ago, but it is now sporting an old Leslie S2, which may have come from one of the old SW1 or SW9 switchers.
A couple of the GP40s have very nice RS5Ts. Again, not sure where they came from -- these units had S3Ls when Guilford first acquired them. It's possible that they actually ordered a few RS5Ts direct from Leslie.
Pan Am Railways — Boston & Maine/Maine Central — Delaware & Hudson
Central Maine & Quebec/Montreal, Maine & Atlantic/Bangor & Aroostook
Providence & Worcester — New England — GE Locomotives