On my Windows 10 tablet I only use touch input for Minecraft. I haven't tried connecting a mouse to see if the Y axis is correctly inverted for the mouse.
This did work correctly on previous IOS pocket editions. I can't remember what version. I can confirm that this is an issue on 'v0.12.1 alpha' on IOS and 'v0.12.1' on Windows 10.
On my Windows 10 tablet I only use touch input for Minecraft. I haven't tried connecting a mouse to see if the Y axis is correctly inverted for the mouse.