The Datasheet says, I can supply 12 to it, but I'm not so sure if I can then directly connect logic to RPi gpio pins.
There are 4 1k pull up resistors (schematic). Should I remove them?
Unless you have an unusual L9110S module it should be fine.
I use these with the RPi without problems.
As they are simpler than the L298N based modules there is much less to go wrong when connecting them up. However, the L298N based modules do have a wider motor voltage range and a bigger current capacity.