Your iPad will normally become warm during use, or when charging. While the iPad will be warm, it should not be uncomfortably hot to hold.
Charging the iPad in a fitted case should not cause any issues - or affect the life of the battery. If you are in a particularly hot environment, or country, then removing the iPad from its case may be beneficial to aid cooling. Your iPad is able to regulate charging in hot environments; if the iPad becomes too warm, charging might automatically stop - and you will see an on-screen warning.
Charge the iPad battery – Apple Support
If your iPhone, iPad, or iPod touch gets too hot or too cold - Apple Support