Employees who are on maternity leave still need to apply for leaves through their Sprout HR accounts. The reason for not automating this feature is to cater to different policies on maternity leave set by every company. Some companies issue maternity leave credits out of their own initiative, while others don't as it is already covered by the SSS.
As a manager, it is best to remind your team members who are taking maternity leaves to apply for the dates when they won't be reporting for work.