To be sure, Nomura does see potential opportunities in the pullback in Hong Kong-listed stocks of China-based businesses, but it isn't alone in seeing broader risks to the territory's market. Goldman Sachs was also already underweight on Hong Kong stocks.
"The latest incident may catalyze an underperforming trend for pure-Hong Kong-based exposure," Goldman said in a note Tuesday, adding it expects that if the unrest persists, investors may demand higher risk premiums.
Read More Images of Hong Kong's violent weekend
But it too sees the risks as bigger than just the latest protests.
"Our cautious view is mainly due to the dual macro headwinds facing the Hong Kong economy, specifically the normalization of U.S. monetary policy that we expect over the next several years and the moderation of economic growth in China, particularly the slowdown of Chinese demand for luxury goods," Goldman said.
Others are also citing concerns that the protests' effects will be longer term than bargain hunters may expect.
Read More How Hong Kong protests affect the big money
"If the current political situation is unchanged for a long period of time, or worsens, the impact could last for the whole of the fourth quarter, which is the peak season for Christmas sales," noted Patrick Wong, an analyst at BNP Paribas, in a note Tuesday. From 2009-2013, 27 percent of annual retail sales of consumer goods were posted in the fourth quarter, he noted.
It's not just a risk for the retail outlets, with Wong noting that property landlords Hysan, Swire Properties, Wharf and Champion REIT all having exposure to retail outlets in the districts affected by the protests.
—By CNBC.Com's Leslie Shaffer; Follow her on Twitter @LeslieShaffer1