Read More Japan shocks as economy slips into recession
"You can say long Nikkei and short the yen is a consensus trade," Tak Aoyama, CIO of $630 million fund of hedge funds AIFAM, said of macro investors.
Just because hedge funds have a bullish trade on doesn't mean they are in it for the long term.
"I started the year hugely bullish on Japan. Hugely bullish, let me say, not qualitatively. I'm not an advocate of the three arrows and the resuscitation to the great heights of whatever Japan represented in the 1980s," Hendry said in a recent interview with MoneyWeek. "I am saying that I can see persistent failure to achieve such honorable ambitions, which leaves no recourse but to intervene again and again and again. Therefore I see the yen being a weak currency ... the other side of that, the stock market, being higher and higher and higher."
Eclectica, which manages $250 million overall, has gained modestly this year in its flagship fund: 2.6 percent through October.
Morgan Creek Capital Management, a Chapel Hill, North Carolina-based investment advisor and allocator to hedge funds, is highly bullish on Japan.
"The events of the last few weeks point to an increasing likelihood that the Japan bull market has far to run before it rests," the firm's CEO, Mark Yusko, said in a recent letter to clients.
Yusko also notes that the government of Japan will continue its stimulus programs because it wants "to show the world that the work of Abenomics is far from complete."
Morgan Creek uses hedge funds like the Indus Japan Fund to express the bullish view. The Japan reflation thesis represents 7.8 percent of its Morgan Creek Global Equity Long/Short Fund, according to investor materials.
Read MoreMore stimulus coming after Japan GDP shocker?
Some hedge fund allocators think the best days of the trade may be over.
"The Japanese equity markets have already moved 100 percent off of the lows—the easy money has probably been made," said Michael Oliver Weinberg, chief investment strategist at Protégé Partners.
Weinberg, who also teaches at Columbia Business School, said he prefers to play Japan through small, Asia-based fund managers who can go long and short.
Aoyama of AIFAM agrees. "We've likely seen most of the effects of Abenomics on Japanese equities and there's not much upside left to the Nikkei," he said.
Aoyama said he isn't giving money to Japan-based hedge funds or others that trade Japanese assets as their returns are too correlated to the market. That includes macro managers who think they can "trade Japan for a quick buck."
One contrarian on Japan is Hayman Capital Management.
The investment manager, led by Kyle Bass, has been critical of the Japanese government and has a dedicated fund to express the negative views. The Japan vehicle uses a combination of short positions on the yen and options on interest rates; it does not directly short government bonds.
Performance of the fund was unclear. A Hayman staffer declined to comment.
Read MoreKyle Bass warns QE end will shake up markets