Saying that a language or language variety marks a grammatical category of "habitual aspect" implies that there is some construction that is dedicated to expressing habitual actions.
"He works" uses the English "simple present tense" construction, which has perfective as well as habitual interpretations. Even if in practice "he works" would typically be understood as referring to a habitual action, this isn't because the verb is marked for habitual aspect specifically: this interpretation is based on a combination of the inherent meaning of the verb work (I think "Aktionsart" is a relevant concept) and the meaning of the progressive aspect, which could have been used but wasn't (that is, "works" is an explicitly "non-progressive" form, contrasting with the progressive form "is working").
Look at the following passage:
First of all, he exhibits a "wonder" by dividing Jordan; then he works a miracle of mercy, by healing the bitter waters; thirdly, by his curse, he brings about a miracle of destruction...
(The Complete Pulpit Commentary, by Henry D.M. Spence)
"He works" in this context does not refer to a habitual action, but to an action that took place at one particular point in time.
The "simple present" often has a habitual sense in Standard English, but it has several other uses that make it inappropriate to call the "simple present" a dedicated "habitual aspect" construction.
For certain categories of verbs that are not widely used in the progressive (e.g. verbs of perception), non-habitual uses of the "simple present" form are fairly common: "I see a spider", "I feel the wind on my face", "I hear a bird calling over there" don't refer to habitual situations.