I like the solution of looking for something in the file to determine whether or not to have autofill.
If you want to put an identifier at the top, you can use code like this:
(defun my-auto-fill-disabling-hook ()
"Check to see if we should disable autofill."
(save-excursion
(when (re-search-forward "Some Unique Identifier" 1000 t)
(auto-fill-mode -1))))
(add-hook 'find-file-hooks 'my-auto-fill-disabling-hook)
And obviously change "Some Unique Identifier"
to something reasonable - such as a search for the tables themselves. Then you'd get exactly what you want, LaTeX files with tables wouldn't be auto-filled.
Note: @Alex suggested using a file-local variable, but this is a mistake according to the manual itself:
Often, however, it is a mistake to enable minor modes this way. Most
minor modes, like Auto Fill mode, represent individual user
preferences. If you want to use a minor mode, it is better to set up
major mode hooks with your init file to turn that minor mode on for
yourself alone (see Init File), instead of using a local variable list
to impose your taste on everyone.