I don't want to state the bleeding obvious here (and I maybe wrong cos it's been a long time) but Stock SH3 had 3 types of Contact marker. 1 x Friendly, 1 x Neutral & 1 x Enemy (for Large, Medium, Small & Individual) contacts. So the correct TGA files are already there. I can't remember if they are in the Textures or Misc folder but for these types of contacts, you should only need to replace these in your current install. Remember, the game knows which vessel is Friend, Foe or Neutral and when.
The only problem comes at higher zoom levels where you can actually see the outline of the ship (i.e xxx_shp.tga). If you want these to be replaced with colour coded icons, you need to individually replace each TGA in each ship folder.
Personally, a good balance would be coloured map contacts with grey ship icons.
The Alpha channels in these TGA's should not govern the colour as SH3 only uses this channel as transparency.