Not doing something mustahabb does not mean that one falls into doing something makrooh in principle, because what is mustahabb comes under the heading of commands and what is makrooh comes under the heading of prohibitions. The word mustahabb refers to something that is enjoined in Islam but is not absolutely binding, such as Duha prayer. The word makrooh refers to something that is forbidden by Islam, but not in a manner that is absolutely binding, such as the prohibition on women following funeral processions. Umm Atiyyah (may Allah be pleased with her) said: We were forbidden to follow funeral processions, but not strictly so.
Narrated by al-Bukhaari, 1219; Muslim, 938
The one who does something that is mustahabb will be rewarded, and the one who does something that is makrooh is not sinning.
Based on that, it cannot be said that the one who does not pray Duha has done something makrooh, just as it cannot be said that the one who does not raise his hands when moving from one posture to another in the prayer has done something makrooh.
Ibn Daqeeq al-Eid (may Allah have mercy on him) said:
We should note the difference between saying that it is mustahabb to do such and such and saying that it is makrooh not to do it. The one does not imply the other. It may be mustahabb to do a thing, but not doing it is not makrooh, such as Duha prayer, for example, and many naafil acts of worship.
End quote from Ihkaam al-Ahkaam Sharh ‘Umdat al-Ahkaam, p. 19
Al-Haafiz Ibn Hajar (may Allah have mercy on him) said:
Not doing something mustahabb is not necessarily makrooh.
End quote from Fath al-Baari, 11/17
Shaykh Muhammad ibn Saalih al-‘Uthaymeen (may Allah have mercy on him) said:
Not doing something that is Sunnah does not necessarily mean that one has fallen into makrooh. Hence if a person does not raise his hands in prayer when bowing, he is not doing something that is makrooh.
This is a basic principle: not doing something mustahabb does not necessarily mean falling into makrooh.
End quote from al-Sharh al-Mumti‘ ‘ala Zaad al-Mustaqni‘, 4/358
And Allah knows best.