That was a production mistake that was later retconned.
https://memory-alpha.fandom.com/wiki/USS_Yamato#Background_information
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https://memory-alpha.fandom.com/wiki/USS_Yamato#Background_information
I've never quite understood why this was a 'production mistake.' How is the registry NCC-1305-E any less valid than NCC-1701-D?
Because the producers said so. It all boils down to the producers deciding to keep a registry number or change it.
Well, that's pretty dumb. I mean, we'd never heard of the Yamato before anyway. So why should it be such a sin that it has an -E registry? Was it some attempt to make the Enterprise iterations special in Starfleet?
I suppose at that point in the franchise they didn't want any other ship to have as many incarnations and suffixes as the Enterprise.
Well, yes, that goes without saying. But it doesn't actually answer my question in any kind of meaningful way.
That's more of an answer. But that seems more like just a changed premise than a 'production mistake.' The latter implies that the writer didn't actually mean to write '1305-E' when he/she in fact did, and it was someone else entirely that decided to change it for their own reasons.
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Had we actually seen a Yamato in a TOS episode or film it would have made things a little easier to swallow, but at that stage in Trek's history it's hard to see any of the producers wanting the audience to think that other ships would be important enough to Starfleet and Federation history to have successive ships sharing the same name and almost identical registry number.
Is it ever stated that the practice was only for the Enterprise?
To my knowledge this was never stated on screen.
Oh, it wasn't a production mistake at all. They just retconned it when they changed their mind.
Even in a fandom that is quick to anger about relatively minor things, would anyone really have been sad if a ship was an ‘E’ at a time when the Enterprise had only hit ‘D’?
Personally I find it adds verisimilitude to the setting.
Personally I find it adds verisimilitude to the setting.
And fast forward 30 years, they've changed it back
I don't really care if the Enterprises are a special case or not, I just want them to be consistent with it!
It's not the weirdest production decision regrading Star Trek I've ever heard, but still it's an odd one.
Hey-ho, learn something new everyday, huh?
Out of universe production reasons? Yes
In-Universe, probably not.
It was a writers room rule at the time of Contagion that only the Enterprise could have a letter. The writer that wrote Contagion wasn't aware of that.
If you read what I quoted, Mike Okuda had even made alternate decals for the Yamato at the time of filming to replace the Registry, but then the scene was removed, so he never applied them, but then it was added again without him knowing so it made it to screen with the the -E registry.
So no-one changed their mind later, it had already been made before the episode was written. Just the writer of the episode wasn't aware of the rule.
The production mistake was whoever reviewed the script not catching it at the start.
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But ‘Contagion’ took place after ‘Where Silence has Lease,’ so that rule wasn’t in effect at the time the scriptwriter wrote the latter story. It was WSHL that the 1305-E registry was stated. Ergo, it wasn’t a ‘production error,’ it was a changed premise.
Little late to be asking for consistency in Star Trek, isn't it?
That ended with "Where No Man Has Gone Before(TOS)." 
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