When early 747's were delivered to their customers, they were equipped with a lounge area on the upper deck, and so were fitted with a 3 window set. With the increase in oil prices in the 1970's, airlines saw the financial benefits of adding more seats on the upper deck, in turn a large number of 747's (both -100's and -200's) were converted in order to have 10 windows to cater for the increase in the number of passengers. For some reason, a smaller number of 747's retained their 3 window status (the French airline Corsair still operate a 747-100 with the 3 window set, as do Air Atlanta Icelandic who operate a couple of 747-246B's that retain their 3 window upper deck).
On your second question about 'Is it possible to identify the difference between a 747-100 and 747-200?'
The answer is yes, on some aircraft...We have already established that it is very difficult to tell a -100 from a -200 by the number of windows, however it can be possible to identify one model from the other by engine type.
Any 747 with CF6 powerplants is a -200 (or 300), as this engine option was offered on the higher gross weight model (-200). Also the Rolls Royce RB211-524D4 powered 747's are -200's, again offered on the higher gross weight 747-200. However Saudi Arabian Airlines operates a number of Rolls Royce RB211-524B 747's that are actually -100's (custom built lower thrust and weight aircraft). It is much more difficult to spot the difference between a P+W 747-100 and 747-200 as the engine design is virtually identical.
Finally, you also say that a 747-300 can be spotted easily...however, some airlines (eg. KLM and Japan Airlines) had their 747-100 and 747-200 aircraft converted with the SUD (Stretched Upper Deck) feature, so they are now technically 747-300's, but the airlines themselves call them 747-206B SUD (KLM) and Japan Airlines 747-146B SUD. Japan Airlines designates a small number of it's 747 Short Range aircraft 747-146BSR/SUD!!
I love it when a plan comes together