There are always going to be some companies that choose secrecy over patents. Coca-Cola has built quite a company around a trade secret formula.
The existance of a few such companies is not a problem, but you are right, where a large percentage of companies cling to secrecy, there is a problem.
A good example of this is the current GPU market, just about everyone is keeping the details of what they are doing secret, in spite of a large number of patents being filed.