If you are able to sell the materials for the potions/ethers, you are still contributing to the economy since that means someone somewhere is making and using them. I've been leveling up off of mega-potions and now mega-ethers, farmed/gathered all the mats and splitting them among my LS, selling the excess on the wards. Obviously if you are already capped Alchemist then you really aren't getting anything for your time if it earns you more money for selling materials instead and that's your call.

It really does depend on your server, though. On Istory you can buy all the materials for Mega-Potions from the wards/NPCs and still turn at the very least a small profit, and really the most "difficult" item to get is the Sagolii Sage. Mega-ethers are similar in that the only relatively uncommon item is the Black Truffle, with the rest of the materials being dirt-cheap or otherwise easy to get on your own. I haven't checked the price on Black Truffles since I gather them myself but they would be the deciding factor between selling them or the finished Ether. If it makes more money selling the Truffles eventually more people will start selling them and drive the price down, resulting in more people selling the finished ethers for a profit.