Is it okay to omit (one or multiple) middle names in a bibliography?
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.