Is there any reason that cross correlation would perform well or poorly on sparse binary arrays?
If you upsample your array to a resolution more than the time uncertainty, or measurement time quantization plus jitter noise, by just zero-filling between events in your event count data, you are adding high-frequency jitter noise that can interfere with correlation results.  You could try upsampling your arrays by using a Gaussian distribution of the appropriate width for each event, instead of just zero-padding between events.  Or, if you have a better statistical distribution for the measurement time offsets/errors, use that.