What are the metrics/quality rules that could be applied on wsdl files ?
There are no Quality Rules defined for wsdl files 
References on CAST Software Platform for measuring software quality

CAST implements its various health factors based on the general guidelines of the ISO/IEC 25010 model. Specific rules and implementation of the guidelines are not provided in the ISO/IEC 25010 model.

We do follow CISQ guidelines which are based on the ISO/IEC 25010 model. You can see more in CISQ Code Quality Standards paper which discusses the alignment of this model with the CISQ standards:

As well as our internal paper discussing the CAST Software Platform measuring these CISQ standards at   Software Characteristics Definition

and our measurement standard documentation: Appendix A - CAST AIP Measurement System explained   

Is is possible to get a quality rule being part of 2 different technical criteria?

Yes, there are some rules that are taking into account in different Technical criteria (with different weight) in the default assessment model  (accessible in CAST-MS)

This is because these rules are considered as impacting different technical criteria/health factor

For further information on this, please refer to the official documentation page about this subject. 

Does the 'Avoid high lack of cohesion' metric understand partial classes?

There is a document that explains how the LCOM (Lack of Cohesion in Methods) is calculated and can be referred from here.

And, to reduce the LCOM the classes should be split into sub-classes. Partial class means to split the classes into several files but in the end the class objects will still be the same and LCOM computation will be the same as well. So this metric does not consider the partial classes because the calculation of LCOM and it's result will be the same as it was originally. 

 Which Indexes (Primary or Secondary) CAST check for the quality rules related to table indexes?
There are some Quality Rules like Avoid SQL queries that no index can support and Avoid Tables having Indexes with a too large Index definition. For the calculation of these rules, CAST AIP checks only for the Primary Indexes. 
 Can we change conditions to activate the metric " Number of Commented-out Code Lines "

No, We cannot change the conditions which need to be met to activate the metric " Number of Commented-out Code Lines ". The complete study of Copy Paste metrics is based on these conditions.

Conditions to activate metric are QRL - Number of Commented-out Code Lines  

Does CAST AIP support java spring-boot for quality/productivity?

CAST AIP doesn’t do any specific analysis related to Spring Boot, but it supports Spring Core.
However, based on what services Spring Boot provides, it is not expected to have any impacts on Function Points calculation: it’s about the application environment, not user inputs or access to data. So that framework should not be used on functional transactions.
For quality, the usual standard JEE/Spring Core rules would apply on Spring Boot as well.