In theory, yes. They mean the same thing.
When you have parenthetical information, you can analyze the essential part of the sentence by removing it—and its removal should result in a still-grammatical sentence.
✔ 1. The two strands of economic theory, which are used in this article, are endogenous growth and spread-backwash effects.
→ The two strands of economic theory are endogenous growth and spread-backwash effects.
❔ 2. The two strands, which are used in this article, of economic theory are endogenous growth and spread-backwash effects.
→ The two strands of economic theory are endogenous growth and spread-backwash effects.
In theory, you can put parenthetical information anywhere because it should have no effect on the surrounding text.
However, in practice, the placement of the parenthetical information is important—regardless of the fact that its placement should have no grammatical bearing.
Here is an extreme case of parenthetical information:
✘ 3. The two strands of economic theory are endogenous growth and spread-backwash, which are used in this article, effects.
→ The two strands of economic theory are endogenous growth and spread-backwash effects.
Nobody would ever phrase the sentence in that way. Despite someone arguing that the placement doesn't matter, it certainly does matter when it comes to a reader's ability to easily parse what's being conveyed.
So, in terms of style, the first sentence in the question is more natural—despite the fact that on strict analysis they mean the same thing.
It's the more natural of the two because if you were to rephrase it as essential information, the order of the words would still make sense:
✔ The two strands of economic theory [] that are used in this article [] are endogenous growth and spread-backwash effects.
Note that it becomes essential information by removing the comma pairs and replacing which with that. (Replacing which is not as important in UK English, but removing the commas is.)
So, use the same order of words as you would if it were essential information, but use a comma pair and which rather than that:
✔ The two strands of economic theory[,] which are used in this article[,] are endogenous growth and spread-backwash effects.