Are Schottky diodes the best option for this application?
Schottky diodes are best used for fast switching application and where the voltage drop due to diode needs to be as less as possible. 
Disadvantage is the high reverse leakage current (and the current is temperature dependent) and lower reverse breakdown voltages.   

If your project is battery operated only and need to save each bit and byte of energy for long term, then opting for normal diode with least reverse leakage current will be better choice.

Also other factors such as price may factor. Schottky diodes are expensive. So, its a trade off among  reverse voltage rating, speed, leakage current and price. So, for your case I would really see further down on the requirement of minimum battery voltage needed for the circuit to operate and battery life time expected. Only, then a good decision can be made.  

Also, if space is not a constraint, opting for PMOSFET as blocking diodes (even NMOS will do) also help in getting out all the juice off battery to the circuit as the forward drop of FETs will be in a few 10s of mV typically.   

Using a diode to ensure current flows in only one direction, without causing a voltage drop