"Is there a way to determine their indices using logical indexing...?"
Yes, and logical indexing is usually a better way to index than using a linear index or subscripts, and you've already discovered how to do it :)
logicalIndex = iList & ~rList & ~dList;
" I've had trouble wrapping my head around how I might achieve that."
Here's a general demo
data = rand(5,10); % random values between 0 and 1
idx = data <0.5; % logical index of values less than 0.5
data(idx) = NaN; % Replaces values < 0.5 with NaNs
