Which of the following is correct?
Data that is stored on your computer will be encrypted if ....
Data stored on your computer will be encrypted if ...
Stored data on your computer will be encrypted if ....
Wiktionary has the following usage note for the word data: "This word is more often used as an uncountable noun with a singular verb than as a plural noun with singular datum."
So it is correct to use the word data with the singular verb is as in your first sentence.
In the second sentence you simply omit "that is", but it is common practice. Wiktionary has the following usage note for the word that: "That can be used to introduce subordinate clauses, but can just as easily be omitted."
In the third sentence it seems like you want to put more emphasis on the word stored.
But gramatically I don't see any problem with any of them.
All are fine to me. It means same thing. But I'd prefer "Stored data on your computer will be encrypted if ...." over the other 2.
hope it helps.