Assessing atomic defect states and their ramifications on the electronic properties of two-dimensional van der Waals semiconducting transition metal dichalcogenides (SC-TMDs) is the primary task to expedite multi-disciplinary efforts in the promotion of next-generation electrical and optical device applications utilizing these low-dimensional materials. Here, with electron tunneling and optical spectroscopy measurements with density functional theory, we spectroscopically locate the mid-gap states from chalcogen-atom vacancies in four representative monolayer SC-TMDs-WS2, MoS2, WSe2, and MoSe2-, and carefully analyze the similarities and dissimilarities of the atomic defects in four distinctive materials regarding the physical origins of the missing chalcogen atoms and the implications to SC-mTMD properties. In addition, we address both quasiparticle and optical energy gaps of the SC-mTMD films and find out many-body interactions significantly enlarge the quasiparticle energy gaps and excitonic binding energies, when the semiconducting monolayers are encapsulated by non-interacting hexagonal boron nitride layers.