@Wraithblade6@Raineh DazeQuick Notes:
1) Gilgamesh has an effectively infinite number of weapons. While there exists a theoretical limit, the amount of shit he can throw at you is in sufficiently high quantity that counting it quickly proves to be pointless. As such, destroying his weapons, with the exception of several particularly potent weapons (Excalibur, Ea, Enkidu, etc.), is mostly pointless.
2) Due to the effect of Gate of Babylon, Gilgamesh can retrieve these weapons pretty much no matter where you send them. As such, the only way to remove them is destruction, which, as previously mentioned, is mostly pointless.
3) Various different weapons display different levels of indestructibility, but all have a baseline strength requiring immense force to actually destroy. Some are capable of reassembling after destruction, or otherwise have specific means of avoiding destruction. Take into account that each of these weapons is a unique magical item, with unique magical properties inherent to that weapon. As such, all will act in different manners.
4) Should you make the weapons sufficiently dirty, Gilgamesh will sometimes leave them behind as having become unworthy of him. He will also often refuse to use his weapons in scenarios that would devalue his treasures in such a manner. Being really disgusting is actually kind of a good counter to him for this reason. An example of this is when he was unwilling to confront the giant tentacle monster summoned by Caster in Fate/Zero, sacrificing only 2 weapons to it, which he refused to retrieve.
5) Magnus easily has the speed and strength required to swat most of these weapons out of the air, and if sufficiently durable that most such weapons would be completely ineffectual against him. For example, a blast from Excalibur's beam effect would only inflict mild damage to Magnus, which would be swiftly regenerated. This is due to Magnus being a Daemon Primarch, and therefore of a scale of being able to walk through nuclear explosions mostly unharmed. It would require some of Gilgamesh's most powerful artifacts to inflict any real damage to Magnus considering this immense damage resistance.
Just a short compilation of my knowledge on the combatants, in relations to each other.
Personal Prediction: Gilgamesh is going to be in serious trouble if he doesn't take Magnus seriously. If he displays his usual arrogance and refuses to accept such a powerful opponent he's going to end up very dead, or with a seriously damaged pride. If he unleashes his full power, even with current limitations, Gil should be able to win, however, even with Magnus' immense power. This is mostly because Magnus has been cut off from his more world-destroying levels of magic, and can no longer stop time.