I want my iPad battery to last as long as possible so considering the fact that I charge my devices overnight will it affect my battery health if I use the 5W IPhone charger to charge my 12.9 iPad Pro? Or is it better to use the bundled iPad charger as it will charge faster meaning less heat exposure?
actually the contrary is true, in both cases:
the faster you charge your lithium ion battery the more heat is potentially being generated and lithium batteries do not like heat (nor freezing temperatures)
while fast charging can normally be safely applied up to a charge rate of 50%, using your iPad charger just means using the charger that has specifically been designed for your iPad's battery. you could use your phone charger, it just would take longer to charge the battery and make your patience wear out way before your battery does
referring to your second statement, charging your battery over night, implies charging your battery to a 100% charge state. lithium ion batteries do not like that either and prefer to be kept at lower charge states which over time will result in higher battery health and higher cycle counts.
Unfortunately most integrated electronics are not designed to stop charging our batteries at a more healthy charge rate of around 60 - 80%, which would be better for long term battery health but let the charge go almost all the way up to 100%, which while not dangerous is not ideal.
http://batteryuniversity.com/learn/article/charging_lithium_ion_batteries
having said that, I do not care about all of this too much and charge my devices whenever I want to whatever charge state it is going to be. batteries age anyway, more or less gracefully, and reach their end of life after 3-5 years, if you use them or not
what really is important though is using the original charger that came with your device. People have been killed by cheap unsafe third party chargers:
https://www.telegraph.co.uk/news/wo...-Australia-killed-by-cheap-phone-charger.html