XLSX files have been around for ... nearly 13-years...
Ugh - I still deal with clients who are creating brand new XLS and DOC files and expecting to have all the latest features (co-authoring when hosted in 365/SharePoint Online/OneDrive/Teams)...
Worked on a world class radiotherapy piece of software. If you like 20 year old Delphi projects and pre C89 ... C, then come over! Xls export is probably a recent addition, xlsx support will most likely come no sooner than when Excel stops supporting xls.
Ten years ago people were still complaining about OOXML not being an open standard. Don't worry guys, I'm sure they'll make a reference implementation of the standard soon! I'm sure there were a few people waiting around for a "real" standard to come out before implementing XLSX support.
I suppose someone had written a VBA macro to import all the CSV files and then save them in a format which could be imported into some dated upstream system. Or never changed how they worked. Could even be because Excel does something slightly more rigorous with XLSX files which made writing the VBA trickier.
I worked with teams integrating legacy systems from hospitals before. There seem to be a large amount of carefully customised scripts for pulling data together. There was never a straight-forward data ETL / export for something other than routinely reported. A lot of information is derived and inferred from even not related (e.g infer chemo events from drug prescription codes if parts of system is not accessible). Hence if you really need high quality data you need a lot of validation and cross-checks as well (either by script or manually). To me it sounds like the checks and validation did not happen enough as the time is very critical. I don't think Excel is the single thing to blame here. Hospital IT systems have a long history of data related issues.
It's also entirely possible that whatever they're importing this data into only supports XLS and not XLSX. I don't think Excel is the ultimate endpoint - the data is getting imported into one or more databases somehow.
My guess: somewhere down the line someone who doesn't often use Excel typed ".xls" at the end of a string variable or selected it from a dropdown list and made a mental note to come back to it if it caused any issues in testing.
Old code is everywhere. I once worked at a health tech startup that was integrating with a very successful existing company. All their code was in Turbo Pascal. We were shocked. The funny thing is that their code worked great and even had a debugger. Our code was ultra modern typescript micro services and we debugged with prints and logs. Their product looked dated but was superior in every other way. My guess here is that XLS is a simpler format and the devs found an NPM package that could handle XLS but not the newer formats.
It may have been a user education and/or communication issue.
I had someone come to me recently asking for some data "in an XLS". I asked them if they specifically need XLS or if they just need something that can be read by Excel. It was the latter, but they didn't know that there was a difference. To some people, XLS == Excel. Sort of like how TLS is still being referred to as SSL - somewhere in the world there is a developer being asked to use SSL for a new project because SSL == secure.
There are a surprising number of people out there that still save their office documents in the old formats for whatever reason they have convinced themselves of. Just a couple weeks ago I had a coworker that sent me a manual for a piece of software he wrote as a .doc file.