All the pronouns with "не-" on the contrary have their stress on the prefix: некто, нечто, некоторый, несколько, негде, некуда, неоткуда, некогда ...
So, the pronunciation of "никто" and "некто" (and all other similar pairs) is very different - they have different stress and different vowels.
The meaning is competely different.

There are 2 classes of "не-" pronouns. The most difficult thing for a non-native speaker is not to confuse those 2 classes.

Class 1 is indefinite pronouns.

Not all the pronouns listed above can be used as indefinite. The indefinite pronouns are: некто, нечто, некоторый, несколько and некогда. They express something unknown, and the meaning of "не-" is close to the meaning of English "some-". There is no negation in this case! They are not negative, they are positive but indefinite.

Most often used are "некоторый" (some, some kind of, some sort of, some of) and "несколько" (some number of, some amount of, several, a few). Both are used with nouns:
Я знаю некоторые арабские буквы. - I know some of Arabic letters. Некоторые люди не любят музыку. - Some people do not like music.
У меня есть несколько газет. - I have several (a few) newspapers. Он знает несколько языков. - He knows several languages.

Then we have "некто" and "нечто", they mean "somebody" and "something" accordingly. Those words are bookish, and not frequently used in colloquial speech (although it is possible).
Некто can only be used in Nominative (no other case!): Некто открыл дверь. - Somebody opened the door. Тебе звонил некто Джон. A John (somebody called John) called you.
Нечто can only be used in Nominative and Accusative (no other case!): Нечто упало с потолка. Something fell from the ceiling. Я увидел нечто странное. I saw something strange.

Note: there is a well-known philosofical question which is rendered in Russian as
Почему существует нечто, а не ничто? (Why does something exist and not nothing?)

As to your example:
В магазине ничего нет. = There is nothing in the shop.
В магазине есть нечто. = There is something in the shop (and I do not know what it is, it puzzles me) - this usage is bookish.

And finally, the indefinite pronoun "некогда" means "once upon a time", "long time ago" and it is outdated already. You can mainly find it in Russian literature: Некогда Россией управлял император. - Long time ago Russia was governed by an imperior.