What is the difference between [Clinical Trials as Topic] category and [Clinical Trial [Publication Type]] category in pubmed?
The actual definitions provided with the MeSH terms look essentially interchangeable:  

Clinical Trial as Topic:
Works about pre-planned studies of the safety, efficacy, or optimum dosage schedule (if appropriate) of one or more diagnostic, therapeutic, or prophylactic drugs, devices, or techniques selected according to predetermined criteria of eligibility and observed for predefined evidence of favorable and unfavorable effects. This concept includes clinical trials conducted both in the U.S. and in other countries.  

Clinical Trial [Publication Type]:
A work that reports on the results of a clinical study in which participants are assigned to receive one or more interventions so that researchers can evaluate the interventions on biomedical or health-related outcomes. The assignments are determined by the study protocol. Participants may receive diagnostic, therapeutic, or other types of interventions. While most clinical trials concern humans, this publication type may be used for clinical veterinary articles meeting the requisites for humans.  

But the difference is simple. CT as Topic refers to publications that talk about Clinical Trials in general, as a subject itself. But CT[Publication Type] refers to an article that is actually reporting the results/analysis of one or many clinical trials.  

To show you what I mean, these are first PubMed results using the two MeSH heading, when you specifically tell the search engine to not include other branching MeSH terms:  

Clinical Trial as Topic:
  

Clinical Trial[Publication type]: