Recently some banks accept the signatures instead of seals (Hanko), but you will still encounter situations where you still you need to use a Hanko.
Originally the Hanko was an invention of the Sumerians, in Mesopotamia, back in BC4,000. In those days, seals were made from clay with distinctive patterns and were used to close off a cylinder containing a document. If the seal was broken, that meant someone had opened the package, and at the same time, the pattern on this seal was good luck charm.
In Japan, they introduced institutional Hankos in the 8th Century, but these died out as the government faded from power. Thereafter, people started using their own handwritten logos, which acted as signatures, called Kao (Flower Seal).
This system lasted hundreds of years, while there was stability and peace in the realm, but once the period of the Warring Sates started in the 16th century, Hanko came back into fashion -- because it was quicker.
Is the role of a Hanko as a good luck charm dead? Well, it's in the ink we use with Hanko. Vermilion ink (Shuniku) is made from vermilion diluted with castor oil. In ancient Japan, coffins were painted vermilion, because it was an excellent bug repellent and preserver, AND in addition it appeared that vermilion had magical properties. Namely, its color turns back to red even after being burned black in a fire. Thus, vermilion became the symbol for revitalization.
Then, how about Kao? We still use these unique signatures for formal documents. For example, the Prime Minister signs after his name on the document approving the choice of cabinet. You can see some examples of early Prime Ministers' Kao.