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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.

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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:

1. Atmospheric conditions prevented landing

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.

2. There were no shuttles

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".

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    It's pure speculation of course, but I like point 2 a lot. They should retcon that in, in a novel or something.
    – Mr Lister
    Aug 30, 2015 at 13:43
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    In my opinion, point 2 makes no sense at all. If the transporter is so reliable and often used, there would be little need to bring visiting shuttles aboard rather than just beam the visitors aboard. But even so, if the frequency at which we see visiting shuttles during TOS is in any way representative, encountering visiting shuttles is an almost non-existent event anyway that would hardly warrant such a comparably large on-board facility as the shuttlebay. If, on the other hand, the shuttlebay is appropriately sized for the amount and frequency of actually visiting shuttles (much might ...
    – O. R. Mapper
    Aug 30, 2015 at 20:29
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    ... happen off-screen ...), it is unlikely that a part of it could simply be occupied with a permanent complement of shuttles without seriously reducing the operability of the ship with respect to visiting shuttles. But even if all of these apply, it still seems very far-fetched that Starfleet should consider the transporter system so infallible that not a single shuttlecraft is available as an alternative, or that no-one would consider the possibility of being unable to transport for external reasons such as atmospheric conditions (certainly, the technical limitations of the system must ...
    – O. R. Mapper
    Aug 30, 2015 at 20:30
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    @O.R.Mapper : For the record, it's not my theory. It's a fan theory that's been thrown around for a while. The question was about whether a canonical explanation exists and the answer to the question is no (as I stated). That's enough to answer the question. I included the fan theories just for the OP's amusement really. :-)
    – Praxis
    Aug 30, 2015 at 23:10
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    @Praxis For what it's worth, the OP was successfully amused.
    – Ixrec
    Aug 30, 2015 at 23:54
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A more functional one is to simply ensure that gap is there for scripting. Otherwise 'it's too easy' and a part of the script is gone.

Scriptors have to take that into consideration, because there has to be a story. The more 'Get Out of Jail Free Cards'in a story for the heroes, the more you eliminate parts of the story. That's why in Doctor Who he loses his Sonic Screwdriver in 'The Visitation' episode.

So it's not always an oversight, sometimes it's deliberate.

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