There are no differences between POM (Acetal, commercial brand name - Delrin) and acrylic glass (Plexi) top in regards to cooling performance. Acrylic is translucent and thus allows the visual inspection of the internals of the water block and for colored coolants to be seen inside the cooling channels.
Acrylic glass can be damaged beyond repair when alcohol or acetone is applied to the surface, while POM (Acetal) offers higher chemical wear resistance.
POM Acetal is softer than acrylic, and its impact strength is higher than the one of Plexi. Plexi (acrylic glass) is more brittle and more prone to cracking when mistreated.