I've always thought the flooding in Lagos could affect a subway. Perhaps Abuja and other states are better suited for undergroundsI really do not think that Underground is well suited for the Lagos terrain (at least not the Lagos Islands and the immediate areas that surround it (Where you have the commercial business districts).
In fact even surface rail is not well suited for many parts of Lagos (so you can only imagine, what you are suggesting by saying underground). It is not an impossibility and there are coastal cities such as New York with underground systems, but there will be complications and increased costs.
New York does face challenges with regards to their underground system.
BTW which 50 Billion went missing? That is a very false assumption.