No that is basically it. Mind you when connecting any hardware to them, you should make sure that they are not pulled LOW through that. A LED should be connected active LOW. (eg Vcc -> LED -> Resistor -> GPIO)
Not really, the Resistor value is quite high, it will work just fine for most things. If it is really an issue, you could pull the current limiting resistor of the board to disconnect the circuit. (or the LED if you want)
Again this is not true. GPIO15 needs to be pulled LOW at boot or the ESP won't work at all, There is a 10K pulldown resistor making sure of this, but for the rest it can be used as normal. It is also an SPI pin and can also be used as part of the alternate UART pins, but will serve also without issue as long as it is is pulled LOW at boot.