That article reads a lot like "Peak Oil" concerns. There is a lot of Helium available - [1] The global reserves of helium are known to be approximately 41 billion cubic meters. Most of them lie in Qatar, Algeria, the USA and Russia. Annual global production of helium is about 175 million cubic meters, and the USA remains the largest producer. "
Regardless, this is something the market can correct for very, very easily. As helium supply becomes more scarce, the price will go up, resulting in greater supply. Most of it comes from natural gas, and is so cheap [2] it's not worth capturing. Oil trades for around $100/barrel. Helium trades at $100 for a thousand cubic feet (albeit in gas form)
Some of the problems with Helium is that Physics experiments use a LOT, and previously was so cheap that it wasn't worth trying to conserve. That's changing - [3] A recycling system can recapture about $12,000/year of lost helium for a single scientist.
From reading articles - apparently the problems isn't so much that the cost of helium is increasing - but that it's been so cheap because of the US Natural Reserves making it completely non-competitive to capture - they are basically giving the stuff away for next to nothing.
[1] http://www.gazprominfo.com/articles/helium/
[2] http://finance.yahoo.com/news/airgas-increase-prices-helium-... And on Friday, the bureau announced that it was raising the price for a thousand cubic feet for crude helium from $84 to $95
[3] http://www.nature.com/news/united-states-extends-life-of-hel...