That's because investors look at Yahoo as a holding company, with 3 main components : Alibaba, Yahoo Japan and Yahoo (USA/Rest of World). It's quite normal that the value of the holding company is (far) below the sum of its parts. There are multiple reasons for this discount: assets are less liquid, overhead costs, management risks, taxes, etc.
Most company have intangible assets and/or liabilities whose valuation is less-than-concrete that aren't traditionally reflected on a balance sheet except when they are given a concrete valuation as "goodwill" in the event of acquisition of the company.
These assets and liabilities exist all the time, though. In the case of a publicly traded company where the market cap is substantially less than the book value -- concrete assets less concrete liabilities -- there is a judgement that these fuzzy assets and liabilities aggregate to a net liability. That's a sign of perceived distress, but not really rare.
Its even less rare for a company to be valued less than its (concrete) assets -- this is fairly normal. That just means that the net positive goodwill is less than concrete liabilities.
only if count the assets (i.e. stocks) at face value.
if you did that, you can just go to any stock market and buy any stock. any. without ever even knowing which company they are for. it is the same reasoning. If you think yahoo has 50b in cash because it has stock of other companies valued at 50b, you can just buy 50b of any company and you will have 50b? probably you are going to have 50b-+(market fluctuation) which is what nobody wants to bet on so easily.