The main problem with the variations of the sentence is the use of both much and many that arrives from the mix of a count noun and a non-count noun.
Also, there are two possible interpretations. One talks about a scarcity of ingredients, while the other talks about a surplus of ingredients.
I will describe the scarcity interpretation first.
Keeping the sentence structure as close as possible to the original, you could say this:
Is there not much sugar or candy in the shop?
This sounds slightly odd, but it is still grammatical and understandable. Note the use of or rather than and. But, primarily, the change of the countable plural candies to the mass noun candy, which allows much to apply to both nouns.
Other ways of phrasing it—although the results are a more dramatic change:
Is there only a little bit of sugar and candy in the shop?
Is the shop running low on sugar and candy?
Does the shop have a shortage of sugar and candy?
In all of these, the mass noun candy from the previous version remains, but or is changed back to and.
Now for the surplus of ingredients interpretation.
In this case, it's a rhetorical question that uses the negative for dramatic effect when, in fact, the opposite is true.
She proudly opened the doors of her well-stocked store. It was brimming with so much sugar and candy that there was barely room to walk anywhere.
"Behold!" she exclaimed. "Is there not much sugar and candy in the shop?"
To make this clearer, compare the final two sentences with this:
"Behold!" she exclaimed. "Is there not a vast amount of sugar and candy in the shop?"
In this context, it becomes clear that Is there not much? actually means Isn't there a lot? But with the sentence entirely on its own, without any such context, it is ambiguous. The use of much after is there not is not normal, so we tend to assume it's talking about a scarcity of ingredients. Yet, at the same time, the is there not construction is one in which the opposite would normally be meant if much were replaced by something else.
Also note that where in the sentence describing a scarcity of ingredients or is used, in this version that describes a lot of ingredients, it goes back to and again.