Is it okay to omit (one or multiple) middle names in a bibliography? Assuming that the cited work will not be less identifiable:
When including a paper in the body and bibliography of one’s work, is it okay to omit the author’s middle name(s) and just give the first and last name in the bibliography?



The main reason why I consider doing that is as follows:

I often cite different works by the same author, but one work lists the middle name, the other doesn’t.

Usually, when two works of the same author are listed in the bibliography, and the names are consistent, they will appear one below the other, and the second entry will not list the author, but a line of dashes:

Doe, John. Work 1, 1999.  
-----. Work 2, 2003.


But if the author is not exactly the same in the bibliography database (in LaTeX, for instance), it will be listed as such:

Doe, John. Work 1, 1999.
Doe, John Jeremy. Work 2, 2003.


This in itself is just cosmetic: it may be bad style, but the bibliography is still correct.

Now imagine there are three works, and only the one that was published between the two others states the middle name of the author.
It would look like this:

Doe, John. Work 1, 1999.
Doe, John. Work 3, 2007.
Doe, John Jeremy. Work 2, 2003.


This is because the bibliographic system doesn’t recognize them as the same author.
This is a problem because the works don’t appear in order of their publishing date.
Bibliography entries should be faithful to the works to which they correspond: you should conform to the constraints of the style used by the journal, but you should not remove or add middle names or initials. The rationale for this is that doing otherwise makes it harder for readers to follow the citations back to the original literature if the names in the article are reported differently from the way they're indexed.

If the same author represented themselves differently in multiple works, that should be reflected in the bibliography entries, even if it makes things awkward for the author citing the works. If you feel you need to indicate that the authors are in fact the same individual, you may do so with a parenthetical comment.