Yes, the sentence is fine grammatically. This isn't just a simple series of unrelated things since there are two types of beans. The first "and" is connecting "honey" and "beans" while the second "and" is connecting "red" and "black." The only thing that's unclear is whether the beans are on the rice cakes or just served at the same time.

'Red and black beans' is considered to be one element, so the rule about only one 'and' in a sequence is maintained. When reading the sentence aloud the first 'and', linking 'rice cakes with honey' and 'red and black beans' is pronounced clearly to indicate that these are separate items, while the 'and' that links red and black beans will be shortened to 'n' : 'red 'n' black beans'

Another example that might help you understand: I like pizza and beer and milk and cookes. Pizza and beer go together. So do milk and cookies. 'I like pizza, beer, milk and cookies' does not communicate the same idea.

Those grammar books are lame, they teach some fake and misleading knowledge in order to keep people from passing exams successfully.

This is an issue of style, not grammar. Your grammar book states that a sentence "should" only contain... Perhaps you misunderstand the meaning of "should". "Should" does not mean the same as "must". "Should" can be more like a recommendation than a command. You are free to disobey recommendations. I cannot say precisely what your grammar book meant by "should". Without reading the grammar book, I cannot know how strong the recommendation was intended to be.