The basic rules regarding enchanted weapons say, that all damage coming from these is inheretly magic.
However, some abilities do change a weapons damage to magic damage of a certain type, like a pladin's smite or a blessing. It is kind of an enchantment that is carried by the weapon but not part of the weapon itself. In case of the smite, a distinction is not really needed, however, there might be cases in which an enchantment that is carried by the weapon for a quite long time. As the makeup of the weapon is not changed, it might not be magical in those cases - but that should be told to the players as soon as they identify it.
Besides this, it might also be the makeup of the 'magical weapon' that might be taken into account when checking if a weapon is magical or not, but you thread on the path to houserules if you do. Ask yourself:
Is it the weapon that carries the enchantment and breaking down the weapon destroys the enchantment xor* is it some other sort of item mounted on or stored inside the weapon that carries the enchantment and would retain the magic no matter of the weapons state or shape?
This could be true for some non-combat related stuff (an example: it might not be the sword but the huge gem in the hilt that is enchanted - break the sword and you retain the gem with its magic) but if this is the case, it is GM fiat, and it should be easily detectable some way or another: in these cases the weapon wouldn't benefit from being protected as magical for example, and again, such an item is clearly not a 'default' magical item as the game gives them out usually.
*eXclusive OR for convenience.