star trek - In TOS: The Enemy Within, why didn't the Enterprise use shuttles after the transporter broke down?

I've heard the out-of-universe explanation is they simply didn't have the props and sets for shuttle scenes that early in the series. Indeed, we don't see any Federation shuttles until The Menagerie, and no shuttles launched from the Enterprise until The Galileo Seven, so I assume this is true.

But is there a known in-universe explanation? I don't recall any characters saying the shuttles were inoperable at the time or the planet had some dangerous atmospheric qualities they needed to bypass via transporter or it would take so long for the shuttles to get down there it wouldn't save Sulu's landing party anyway.

Answer

There has never been an official in-universe reason given by anyone associated with that episode in particular or with Star Trek in general.

It is, however, an issue that has been discussed for years and years by Star Trek fans. Here are two in-universe fan theories that have been tossed around for a few decades:

You've already alluded to this one in your question. Although not mentioned explicitly in the episode, the harsh weather developing around Sulu's landing party might have been part of wider atmospheric disturbances — piloting through the atmosphere may have been next to impossible.

Perhaps there were no shuttles and the Shuttle Bay was intended to be used mainly to bring visiting shuttles aboard rather than to deploy shuttles belonging to the Enterprise, partly because of how reliable the transporter had become by 2265. It could be that the incident in "The Enemy Within" actually led to a request for a set of Starfleet shuttles to be permanently placed on the Enterprise, leading to the use of one in "The Galileo Seven".