Has scholarship shown that persecuted religious minorities have tended to be financially successful?

I think Stephenson has the cart leading the horse here.

Take the Jews of Western Europe (Jews in Eastern Europe were emphatically not well off). The Jews did not became wealthy because they were persecuted. To a large extent, they became wealthy because they could be bankers (and could loan money, even if not formally bankers) at a time when Christians were forbidden to be, because of the Church's attitude was that usury was sinful. Their subsequent wealth led to further discrimination.

Generally I would say "no". The exception of course being the Abrahamic religions Judaism, Christianity and Islam, which prohibits taking advantage of "brothers" (those with the same faith) by charging interest - this obvious opened up a nisce for minorities of other faiths.

But it's not as clear cut, as - to take Europe - Jews didn't only lend money to Christians, there were also Christians who let money to Jews... the important thing, was not to lend to people of your own faith. Of course since there were fewer Jews in Europe than Christians, the wealth from this where most obviously accumulated among the relatively few Jews.

Minorities were often heavily taxed - both Jews in Christian Europe and non-muslims under Islam. Further more, minorities risked having their whole fortune sieced, being arrested or expelled.

If you look at other minorities - especially non-religious or at least not Jews or Christians - they have not fared well at all.

Yale Professor Amy Chua makes this case for Russian Jews, Yugoslav Croats, Chinese in Southeast Asia and others, in this book http://en.wikipedia.org/wiki/World_on_Fire

Note, however, that she is also the author of "Battle Hymn of the Tiger Mother."

The Chinese minority in Indonesia is the first supporting example that comes to mind. However worldwide it is far more common for oppressed ethnic minorities to be relatively poor due to the legal and social barriers they have to deal with.

I love Neal Stevenson's work (particularly the Baroque Cycle), but like many authors he's got his annoying quirks. In this case he's made the classic error of believing the plural of anecdote is "data".

Is there any evidence for this statement?

No. It is clearly falsifiable and falsified—see the experience of indigenous people in settler societies. (Think Canada, US, Australia, New Zealand, Argentina, Chile).

Here is a relevant example concerning the Jewish minority in late 19th-century Vienna, as recorded by Peter Gay in Freud: A Life for Our Time:

Many of the immigrants from the miserable villages to the east dressed and spoke and gestured in ways alien and disagreeable to the Viennese; they were too exotic to be familiar and not exotic enough to be charming. They came as peddlers and small shopkeepers, but many of their sons entered callings vulnerable to bigoted criticism and easy slander: banking, or wholesale trading, or journalism. By the 1880s, at lead half of Viennese journalists, physicians, and lawyers where Jews. [Sigmund] Freud at Gymnasium contemplating either a legal or a medical career was being perfectly conventional. That is what many young Jews in Vienna did. Demonstrating their proverbial appetite for learning, they poured into Vienna's educational institutions and, concentrated as they were in a few districts, clustered in a few schools until their classes resembled extended family clans. During the eight years that Freud attended his Gymnasium, between 1865 and 1873, the number of Jewis students there increased from 68 to 300, rising from 44 to 73 percent of the tool school population.

IMO the phenomenon is clearly not restricted to Jews and to followers of the Abrahamic religions alone (as suggested in another answer): To some extent it e.g. also applies to Chinese minorities in countries such as Indonesia (as I know from a friend's family history), to Indians in Africa (V.S. Naipaul's novel A Bend in the River conveys a bit of that), and to Asian-American students excelling in top graduate schools today (let's not forget that their forefathers once were also confined to "persecuted minorities").