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The check for the Silph Scope revealing unidentifiable ghosts is located in two places in the ROM, one for the Marowak fight and another for all the Gastly/ Haunter you find in the wild. I'm not good enough with ASM to completely bypass the check, but its pretty easy to change the item that the routine checks in order to reveal the Pokemon. The item ID to be checked when fighting the Marowak is loaded at 0x7F94C, while the item ID for wild Pokemon is loaded at 0x7F6F8. When you go to those locations in a hex editor you should see that the bytes at those locations read '67 01', which is the hexadecimal value for the Silph Scope (0x167). To change which item should be checked, just change those values. Since I'm not good enough to bypass it, my advice would be to change the item the functions are looking for to another key item that the player is required to get earlier in your game. This could be something like the Teachy TV or a HM; so long as the player can't avoid getting it and they can't throw it away. It's not a perfect solution, but its a workable solution :P
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