How does SMF5.0A compare with SMF6.0A — which one should I choose?

The key difference is the stand-off voltage. The SMF5.0A has Vrwm of 5.00V and breakdown range of 6.40-7.00V, optimized for 5V DC rails. The SMF6.0A has Vrwm of 6.00V and Vbr of 6.67-7.37V, designed for 6V-tolerant circuits. If your circuit normally operates at 5.0V nominal with ±5% tolerance (4.75V to 5.25V), the SMF5.0A is the correct choice. If the nominal rail voltage exceeds 5.25V, consider the SMF6.0A or next higher voltage variant.