They are not decisive proof but there is little reason to believe the legend of these two alterations. I'll copy here what has been said so far by some:
the number on the side of the prop is D-138, whilst the Hindenburg was D-LZ129
(this at least prooves that there was no intention to make it the "famous" Hindenburg to begin with, if it was decided later in the post-production who knows... but there is nothing in the archives suggesting a different version)
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Something about the first look at the zeppelin immediately made me laugh, because things have a habit of blowing up around Indy and people knew the eventual fate of the airship. I also remember I wasn't the only one in the theater to make that connection and laugh.
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I saw Last Crusade during the first week or so of its release. I have a pretty good memory and would definitely recall if the zeppelin in the movie was named Hindenburg.
I do have a pretty specific recollection of the "donated by" line because of its calculation to get a "yeah right" reaction, and there was no mention of the ethnicity of the "donors."
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I saw this when it first came out and remember expecting it to be the Hindenburg and then being surprised that it wasn’t. Though I bet it was supposed to be at one point in the creative process.
The script also says nothing about Jewish families (nor Zeppelin model)
DONOVAN Precious valuables, Your Highness, "donated" by some of the finest families in all of Germany.
The inverted commas around the word donated are self-explanatory and required no further underlining. "Jewish" would have been an over-kill to the whole dialogue. In any case, considering that here is more evidence towards the non-existance of an alternate theatrical version, I find it hard to hypothesize a different version just based on recollections from people who more than likely expected to hear that line or see that name then their immagination filled the gaps becoming a memory. Especially when there are accounts of people expecting to hear/see those elements and being disappointed for not finding them in the film.