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Not a long post, but something I found little reference to.
I have been working on a project that uses the NodeMCU v1 board to drive a couple of transistor based outputs. The project uses a battery, so I was keen to keep the module in DeepSleep() for as long as possible.
It turns out however, that contrary to what is stated in the ESP8266 datasheet – the GPIOs do not hold their state through DeepSleep(). For me the pins I was using went high during sleep, turning on relays and LEDs galore. I found that a fairly stout resistor would pull them back down during the sleep, without impacting normal operation – but this added a couple of milliamps to my sleep current, and seemed wasteful to have the board sit burning current in a resistor.
A little exploration found, for me at least that D0-D4 would always go high during sleep, but D5-D7 actually held their state. So far this has worked for several weeks, and quite a bit of testing.
So if you are having this problem, maybe try using the higher numbered outputs!