There are versions of the Atari 520ST, and perhaps the 1040ST, that differ in having many discrete inductors attached at the I/O port lines for serial, parallel and floppy ports.
Essentially all later ST have them. The first picture shows a C070115 Rev. 2 ST board wich is about the oldest in general availability. The second is a C070243 Rev. C which is the direct follow up (*1). This and all later 520 models had them added.
Are the inductors unnecessary, and were removed to save cost?
It's rather the other way around, as they were inserted later.
Are was this a correction that added the inductors to solve some complicated line noise/standing wave or similar "complicated EE problem"?
The chokes are to reduce EMC insertion as well as emission. Atari seemed to be very afraid about noise insertion at that time and it may be past of lesson learned from early units. Just open any Floppy and you'll note as well a way larger number of chokes than one would expect. Not to mention additional ferites.
A friend of mine jokingly called them Angst-Drosseln (*2) as he assumed them to be more meant to throttle the designers Angst about EMC than real EMC.
*1 - There were inbetween designs, but I'm not sure if any o them went into production
*2 - Drossel is the German EE term for choke/throttle but also meaning strangling (as in Erdrosseln). In a play with German Grammer the second meaning might be translated as "dampening the fear" :))