I will use a battery as a power source and I would like to know some
way to limit the current charge of the decoupling capacitor so as not
to consume the battery so quickly
It makes no difference how quickly or slowly you charge the capacitor via a resistor. And it doesn't matter whether it's a trace resistance, a real resistor component or the internal resistance of the battery because, the energy put in from the battery/source is \$C\cdot V^2\$ and, the energy acquired by the capacitor is only \$\frac{C\cdot V^2}{2}\$.
In other words, 50% of the energy is burnt each time you charge the capacitor up to the battery voltage from a discharged state.
There are more sophisticated ways (using a buck-boost converter) to save that wasted energy but, it's possible that the small inefficiencies of the converter (over time) will outweigh the energy savings you might make.
how can I calculate the initial current to charge the capacitor?
Use the battery's internal resistance (effective series resistance or ESR) and the ESR of the capacitor to estimate the peak current.
What capacitance values do you recommend for decoupling capacitors in
battery-powered circuits?
It's purely down to how much "instant" energy is required for each chip or sub-circuit. Decouplers are used to provide localized short-term energy dispensers thus avoiding long power lines carrying these currents. This reduces EMI (due to long trace inductance) and localized short-term voltage droop that might disrupt circuit functionality.