Kindly let us know the MDM version .
Check from cmxserver logs , if any other query is being executed on CMX_ORS.T$_STN_BO_CUST on which this index creation query is waiting. You might also needs to look into Db logs to understand the cause of this in case this is happen frequently. I believe you can give the job a try after recycling the App Servers.
Please refer to the below KB articles:
You can refer to the video KB on best practices for MDM performance:https://youtu.be/2By3561owMA.
Apart from these, You can also improve the tokenization job performance by unselecting the Allow Missing Child Records option. (if that's the case)