When I decide what the loot goals will be in my missions, I consider ONLY loot which is not found in secrets. IMO a player should be able to fulfill the loot goal on Expert without finding ANY secrets and it should never be more than 80%. My rule of thumb is usually 50-60-70% or 50-65-80% of the total loot not in secrets for the loot goals, rounded up to the nearest 100. My objective is for the player to generally have already fulfilled the loot goal by the time they finish all the other objectives (or be very close), because backtracking and searching for missed loot once everything else is done is not fun, and is also something Garrett wouldn't bother to do most of the time.