What “Apple Script” did you use? Exactly how did you import the file into DEVONthink? What makes you think that the the file was changed from tab delimited to comma delimited? Do any or all of the files you mention actually have a header row (looks like the view just assumes first row is a header, which is reasonable). How is what you see different than what the DEVONthink Manual (page 46 of for version 3.6.3) says about CSV files?
I never looked at a CSV file in DEVONthink before. So I tried it with one of mine that was comma delimited and coincidently was from my bank. Yes, it displays the file as a table, using the first row as a header. After import, I also did a “open with” command to view the file that was inside DEVONthink with a text editor, and the delimiters were still commas. No changes to the source file.
I did a search/replace-all commas in the file to tabs, resaved as a new tab delimited file on Desktop, then imported into DEVONthink (drag and drop). Same results–viewed the file as a Table and there were no modifications to the delimiters.
So, if there were changes it must have been due to the Apple Script file you ran on the file? No?
Update Friday, 2 April 2021 at 06:57:00 BST: I edited the comma-delimited version of the file (using the open with a text editor) and removed the top header line. After saving the file, DEVONthink recognised that there was no header row and renamed the headers “A”, “B”, … Same result with doing the same experiment with the tab-delimited version. Can detect no changes made to the files by DEVONthink, as expected.