“How do you like your eggs?” usually means “How do you like your eggs prepared?” A popular joke is:
   
Waiter: How do you like your eggs?
Diner: I don’t know. I haven’t gotten them yet.
   
The eggs joke has been cited in print since at least 1933.
 
“How do I like my eggs? Umm, in a cake” is another answer to the ‘How do you like your eggs?” question.
     
   
Google Books
Loss Control
American Mutual Liability Insurance Company
Volumes 11-14
1931 (This Google Books date may be incorrect.—ed.)
Pg. 22:
Likes ‘em Tasty
Waitress (taking order): “How do you like your eggs?”
Diner-to-be: “How do I know? I haven’t had them yet!”
   
18 July 1933, The Evening News (Wilkes-Barre, PA), “The Office Cat” by Junius, pg. 8, col. 7:
Waitress (taking order)—How do you like your eggs?
Customer—How do I know? I haven’t had them yet.
 
Google Books
National Petroleum News
Volume 25
1933
Pg. 65:
Waitress (taking order) — “How do you like your eggs?”
Customer — “How do I know? I haven’t had them yet.” — The Unloading Rack.
         
21 June 1996, Roanoke (VA) Times, “Literal Translations” by Nancy Gleiner, pg. 1:
“How do you like your eggs?” Hard to tell; you don’t have them yet!
 
Twitter
Sauganash Steve
@DartTalk
I’m ordering breakfast…
Waitress: “How do you like your eggs?”
Me: “Dunno. Haven’t had them yet.”
Waitress: You’re getting liquid chicken
7:31 PM - 24 Aug 2016 from Chicago, IL
   
Twitter
grayosn
@graypsoda
Dad:  I’ll have the 3 eggs with bacon and orange juice.
Server:  How do you like your eggs?
Dad:  I don’t know.  I haven’t had them yet.
10:54 PM - 6 Oct 2016
   
Twitter
James Mcdonald
@soggywafflejam
When someone says “how do you like your eggs?” My dad says “I don’t know, I haven’t had them yet.” #MarchDadness
10:15 PM - 15 Mar 2017
   
Twitter
mike Knight
@claytonedge
Replying to @FeelGoodContact @Superdry
Dad at breakfast: I’ll have the eggs & bacon w/ orange juice.
Server: How do you like your eggs?
Dad: I don’t know. I haven’t had them yet.
4:41 AM - 9 Jun 2017
 
Reddit—Jokes
Dad at breakfast:
submitted June 17, 2018 by Athens01
Dad at breakfast: I’ll have bacon and eggs, please
Waiter: How do you like your eggs?
Dad: I don’t know, I haven’t gotten them yet!