Can WinWedge be configured such that, for example, 32 consecutive values out of every thousand are passed to the target application, with the remainder being ignored?

Yes WinWedge can if, the target application has macro/scripting capabilities (such as Excel, Access, Word, etc.).  It would be a simple matter to develop a macro in one of those applications, which would log the first 32 records received, ignore the next 968 records, and then repeat the process indefinitely.  The possible issues I see are:

1.  If the transducer output records are extremely large and/or extremely frequent (e.g., 100 records per second), they may exceed the ability of WinWedge to keep up.

2.  If the ultimate target application does not have macro/scripting capabilities, you would need to use Excel, Access etc. as an intermediate step to log only the desired records, and then process the resulting file later with the ultimate target application.