Should I drain water after I cook noodles in microwave

similar to what julio said, the main reason is that typical wheat-based noodles release a lot of starch into the water, which changes the consistency of the soup. the starches can add a dirty colour to the water, but more than that, they can also thicken the soup undesirably (think of making a roux). Finally, if there are leftovers, the noodles can sometimes become completely water logged, making eating it the next day a bit of a soggy experience.

That said, with all these considerations there are times when you might add the noodles directly in-- non-starchy noodles (eg. like rice noodles) seem to do ok. also parboiling regular pasta before hand seems to help a lot with the starch and can still help you achieve the flavour integration you mentioned.

It's not too much water that makes them soggy, it's cooking them for too long in the water. Thin noodles are virtually done as soon as they break out of their dry, tablet shape. As soon as this happens, take a noodle out and test it. Remember that cooking will continue even after you drain the noodles.

You should drain the noodles well in a colander. If you are planning on stir frying the noodles, you need to first wash the starch off them - run the cold water tap over them and circulate it through the noodles with your hand (carefully, they might still be hot in the middle). They then need to be dried as much possible - spread them out on a board, pat with paper towel, and leave for ten minutes or so before stir frying (preferably in an empty wok - cook the rest of the stir fry first, then empty it, cook the noodles, and re-add the meat etc.)