Yes, when you repeat a word at the beginning of successive phrases, there is a proper grammar to use. Specifically, you need to make sure that the phrases that follow the repeated words are expressed in a similar form or pattern. This is parallel construction. In your sentence, part of getting the parallelism right means making sure that each phrase describes the same thing.
Your first two “something” clauses are okay -- radioisotopes are “something to be frightened of, something with ominous powers.” But the third clause doesn’t work -- “something that is an unseen ninja equipped with a poison beam gun.” The pattern of the words there is wholly different, and the metaphor becomes strained to the point of incoherence. Radioisotopes aren’t like a ninja. If you must use the metaphor, they are more like the beam emitted by your ninja’s gun.
The ninja metaphor isn't really worth saving, but if you mean to keep it, try repeating “something” just once and then make the metaphor explicit:
The effect is that radioisotopes are often thought of as something to be frightened of, something with ominous powers, like rays from the gun of an unseen ninja.