sounds like your patio was laid on sand and sand brushed over the top. over time the sand has washed away and silt etc. moved in. this is very common. weeds will always be an issue unless you pull up the stones and morter them in. however, if you use a non-selective type herbicide in combination with a pre-emergent product every 3-4 months, your weed problems will be few. i recently pulled up some flagstones and spread about 2 inches of dry morter, relaid the rock, and broomed morter over the cracks and then lightly watered untill the morter was wet. i let it set up and it seems to be working fine. this is a short cut method and may not last forever.