Replacing esse with a dash does not feel like idiomatic Latin to me.
One important reason is that the dash did not exist in the era of classical Latin, at least not like today.
Using a dash instead of a "to be" is common in Russian (and maybe other Slavic languages), and I have seen a number of people who were educated in Russian using dash similarly in English and other languages.
Therefore option 1 looks like Russian influence to me, and I don't think it sits as well with Latin.
A much more idiomatic choice in Latin is to leave out the esse completely.
Option 2 feels more idiomatic.
However, it doesn't mean "bad thoughts give rise/lead to bad results".
It means "bad thoughts are bad results".
In fact, option 1 might be preferable as the dash could be read as "therefore" instead of a form of esse.
I prefer option 3; something else would be better.
I agree with Hugh that "ex X[abl] Y[nom]" is a good way to translate "from X Y".
No verb is needed.
If you want to add a verb, it should not be esse.
The English original has "give rise" or "lead to", not "are".
A better fit would be fieri:
E cogitationibus malis praemia mala fiunt
From bad thoughts arise bad results
One can also rewrite the whole sentence to get more options:
Mala cogitans mala facit
One who things bad does bad things
Here you can replace mala ("bad things") with male ("badly") in one or both instances.
Per cogitationes malas male accidit
Through bad thoughts bad things happen
The difference between these two options is whether you want to give more agency to someone doing bad or the bad events themselves.