With the iPad 2 flying off shelves for a second time Wednesday, things look great for Apple right now. But at least one analyst sees dark clouds looming over the company’s record-breaking run.

JMP Securities analyst Alex Gauna downgraded Apple from “market outperform” to “market perform.” According to the full-text of the memo (h/t Business Insider), Gauna said that there is a “notable deceleration in (Apple’s) primary manufacturing partner Hon Hai, the parent of Foxconn, that was emerging even prior to the amplified uncertainty created by developments in Japan.”

The earthquake and tsunami that hit Japan have some technology companies worried about their supply lines, but Apple has said its supplies are fine. The company has delayed the planned March 25 Japanese launch of its tablet while the country focuses on recovery.

According to Gauna’s numbers, Hon Hai’s growth decelerated 84 percent year-over-year in December, 37 percent in January and 26 percent in February. He also said that iPhone sales are “tracking simply in line” for the March quarter, and that the iPad may cut into computer sales.

Gauna trimmed his estimate for Apple’s March quarter revenues from $23 billion to $22 billion. Barron’s notes that that estimate is in line with Apple’s own projections.

Demand has stretched the company’s supply of the iPad 2 thin — the company Web site said Wednesday morning to expect iPad 2 orders to take 4-5 weeks.

Apple shares had dropped a little over 2 percent as of 11 a.m. Wednesday.

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