Most good rechargeable devices, such as your DSi, shouldn't be warming up that noticeably only due to long use. Even after several hours of use, the battery shouldn't be like that. So yes, it's bad. However, it is normal for heating up to happen when it's recharging--especially when it's finished, but still plugged in.
To avoid the above case, be sure to unplug it as soon as possible.
But if you're right and your DSi is actually getting warm when used for a long time, it may be that your battery's capacity is becoming low--in which case do consider replacing it.