The NPC does make it very clear to you during the dialogue that "please make sure you do not have any outstanding quests as these will be unable to be progressed if you accept this new one" I guess its easy to miss if you are skipping through the dialogue but you defiantly get some form of warning.
Both. The shops update their stock as you go through the game so its worth checking every now and again to look for the "NEW!" icons in their inventory. But you do find better pieces than the shops offer every now and again (Gryphon Armor comes to mind).
In theory its possible to complete the game at lvl50 as a Fighter if you wanted. Ideally you want to wait until the profession is maxed (all the red wax seal symbols are full) this means you have unlocked all skills to purchase for that profession. Then switch to a new one and start the process again, depending on what you switch to some of the Core skills carry over and become useful bonus's to your new profession