How to reproduce

1. Place a minecart with command block
2. Leave and reopen the world
3. Destroy it in creative mode using your hand, a sword / tool or an arrow
   → The minecart with command block drops a (regular) minecart (item) named "@", whereas an empty / normal minecart would’ve dropped nothing after these steps. Also if you don’t leave and reopen the world first, the minecart with command blocks drops nothing either.

Code analysis

The following is based on decompiled version of Minecraft 1.8 using MCP. All method and class names are the names used in the decompiled version.

The reason why this happens is that the public void writeDataToNBT(NBTTagCompound p_145758_1_) method of the net.minecraft.command.server.CommandBlockLogic class always saves the CustomName in the NBT data. As this only happens when you unload the minecart or reopen the world a MinecartCommandBlock that is summoned and directly destroyed does not cause this. Instead the method should only save the CustomName if it is not "@".

/**
 * Stores data to NBT format.
 */
public void writeDataToNBT(NBTTagCompound p_145758_1_)
{
    p_145758_1_.setString("Command", this.commandStored);
    p_145758_1_.setInteger("SuccessCount", this.successCount);
    
    // Replaced this
    //p_145758_1_.setString("CustomName", this.customName);
    if (!this.customName.equals("@")) {
        p_145758_1_.setString("CustomName", this.customName);    
    }
    
    p_145758_1_.setBoolean("TrackOutput", this.trackOutput);

    if (this.lastOutput != null && this.trackOutput)
    {
        p_145758_1_.setString("LastOutput", IChatComponent.Serializer.componentToJson(this.lastOutput));
    }

    this.field_175575_g.func_179670_b(p_145758_1_);
}