Some mods will conflict, others won't. You should sit down with your GM and consider this - does the Hi-Power mod, by nature, require easily-detectable parts, or is it just a different shape?
Some mods are a no-brainer. The appearance mod is, by its nature, bulky and noticeable. You just aren't getting a Trekkie Phaser through security without some fast-talking. On the other hand, a Weapon Focus isn't any more visible to a scanner. The wagemage, however...
Things like the Smartgun system, generally no issue. Redundant Process Manufacturing? That's gonna show.
What mods do you have in mind?