Yes, after it rains, you should reapply the natural repellents.
The rain is likely to wash off some of the products from your yard. Natural products are intended to be used over time, so it's safe to use them again after a rainstorm. In addition, rain is beneficial because it allows for additional scent dispersion that may come with some organic or natural brands. It also helps break down any mulch and spread ground-covering plant material around the property while doing water bills savings by increasing runoff rates and improving drainage on concrete and other hard surfaces exposed to direct rainfall (increasing permeability). A bit of added exercise can go a long way!