Is Dr. Ned Dr. Zed in Disguise or is This Simply a Recurring Gag?

Solution 1:

It's definitely him.

"My brother, who is most definitely not me in disguise"

This is a classic case of Suspiciously Specific Denial, a trope which is typically either used to make it obvious that the inverse of what the person is saying is true, or subverted to make people think it's suspicious and later reveal that it was all true and the character was just bad at talking about it.

This isn't confirmation on its own since they could be subverting the trope, but the trivia section on the wiki page for Dr. Ned states:

After he is killed, his name tag will say "Zed" not "Ned" and his mustache will be missing.

So it was definitely Dr. Zed in a Paper-Thin Disguise.

Solution 2:

He is Dr. Zed's brother, NOT Dr. Zed himself. In the Game of the Year Edition Guide from Brady Games, it is stated that he is indeed "the evil twin brother of Fyrestone practitioner Dr. Zed." This actually is referred to again, jokingly, in Borderlands 2, during the mission "Monster Mash (Part 3)". When turning in the mission to Dr. Zed, you are shown a mission completed paragraph that reads "If you think Dr. Zed is creepy, be glad that you never met his brother." The joke here being that although the Vault Hunter you are currently playing as has never met Dr. Ned, that people who had played The Zombie Island of Dr. Ned DLC for Borderlands 1 will remember the creepy Zed lookalike.