It might help to understand the grammatical terminology behind the two alternatives.
In motorized transport, motorized obviously is an adjective modifying the noun transport. In motor transport, motor is called a noun adjunct or attributive noun, much like in chicken soup or football player and is used in the same way as adjectives are.
While there are no common alternatives using adjectives instead of attributive nouns in compounds like football player there often is more than one way of expressing something. On its entry to attributive noun wikipedia gives the example that both erythrocyte maturation (attributive noun) and erythrocytic maturation (adjective) are common and valid terms for the same process. Thus, the availability of a valid adjective does not necesarrily need to keep you from using an attributive noun in its place.
That said, I would consider both alternatives, motor transport and motorized transport as equally valid synonyms.