The pullups are connected to vcc 3v with 4.7k resistors, about 500uA extra current is lost after this addition. After an i2c transaction, the i2c block is disabled, and device sleeps to save power. The behavior is normal by standards of i2c since the pull-ups job is to hold the line high, but because it is in low power mode, the block gets disabled and I assume the lines will need to be configured in a way that they don't draw current when idle?
A real I2C block won't have (fixed) internal pullups as this would contradict the idea of I2C (external pullup, open drain outputs -> 3.3V/5V tolerant). Actually true I2C peripherals don't have a push/pull stage configured to use only the lowside, but a true open drain output. So e.g. they can tolerate 5V on a 3.3V device even if no voltage is supplied. Indeed, for the same reason, true I2C pins typically also don't have configurable pull devices.
Besides, pullup/down configuration is typically a port/pad/pin feature, not one of the peripheral block. Anyway, the behavior of pull devices during powerdown depends on the device and the powerdown mode. Typically, pull devices are deactivated (only) in deep powerdown but still active in sleep mode. Again, that depends on the actual device and its powerdown/sleep modes.
In any case: if you're using normal port pins as I2C pins, make sure to configure them as open drain and to disable any internal pull device. Also check how the powerdown behavior is defined exactly and if you could also use dedicated I2C pins.