Is the 5mm spacer literally 5mm thickness. I bought a spacer long time and never use it but when I measure it is only 3mm. If I use spacer is the torque specs on lug nuts is the same?

Spacers should be what they say. So yes a 5mm should be 5mm. Sounds like you have a 3mm. Basically a shim. I would torque that to 100ft-lbs, you’ll be fine with a 3mm.