In Destiny 2 if I put an armour mod into some armour and later dismantle it, will the mod be destroyed? I am wondering if I should wait on using my mods until I have raid ready gear.
Yes, the mod gets destroyed with the armor/weapon, you don't get it back.
There's no reason not to use mods on your gear though, as once you have over 280 power, you can combine mods into stronger mods and your only limiter is going to be glimmer. You can still save your best mods for raid gear though.