Meaning
See you in the funny paper[s] means "Goodbye, see you soon".
A Dictionary of Catch Phrases (1986) by Eric Partridge and Paul Beale says:
see you in the funny papers (—often and orig. I'll). 'This jocular farewell suggests that the person addressed is rather laughable: US: 1920s; extinct by the 1950s' (R.C., 1978). Perhaps adopted in the UK from American servicemen c. 1943. By c. 1955, (I'll) see you in the funnies.
Etymology
The OED has funny paper from 1874 and funny column from 1860, meaning "a (section of a) newspaper containing humorous matter or illustrations".
1920
The earliest example I found of the phrase is in a letter in Commercial Telegraphers' Journal (August 1920, Vol. XVIII, No. 8):
So long, boys, see you in the funny paper. "30."
J. N. HANNA,
Box 1004.
1921
Another in the Union Postal Clerk (March 1921, Vol. XCII, No. 3):
We will see you in the "funny paper" next month.
PRESS COMMITTEE.
1921
Here's a April 15, 1921 letter published in University of Virginia student paper The Virginia Reel (April 18, 1921 Vol. 1, No. 8):
Well, boys, must close now. La, la, till the next time, and I'll see you in the funny papers. Ever your, ADELAIDE.
1922
Here's a 1922 example in the signoff of a report in The Tusla Scout from Troop 12 by Ed M'Lain (published in The Tulsa Daily World, March 19, 1922):
Good-bye, see you in the funny paper.
This use by scouts suggests it's not insulting, but may be used in a good-natured, light-hearted mocking manner.
In my opinion, the adverb enough used in this sense creates a conversational rapport between the speaker/writer and listener/reader. In strangely enough, interestingly enough etc., the enough might mean "enough to go so far as to consider it such". The reason it's used is perhaps a fear that the addressee might not feel the described circumstances really warrant the qualification strangely/interestingly/etc. By using it, the speaker/writer acknowledges that their listener/reader is right to think that, but that the circumstances really can be considered such for the sake of their conversation.
In any case, this enough is not used in a formal register. When it is used in a formal setting, it signals a (temporary) lowering of the register.
Just my two cents.
Best Answer
Funny in this case just means strange, or unusual; and, notwithstanding Rushdie's deft use of alliteration, a fish just means a thing, as in "a kettle of fish". So, a funny fish is just a strange thing:
The use of fish brings to mind Shakespeare's phrase a cold fish, to indicate a heartless person:
A Winter's Tale, Act 4, Scene 4
Also, there is the phrase kettle of fish, where fish refers to some unspecified object. See: Origin of “kettle of fish”.
Cambridge Dictionary