Sorry, I have not used Veeam... But I can tell you that load balancing on the MX is flow based. I.e. each source port/IP dest port/ip stream will be load balanced to a link based on Meraki's fancy algorithm. If the backup is one flow containing the entire backup job then that flow will use one path and only one path. But, if the backup uses multiple flows then it possible each flow could use a different path. The more flows the more even the distribution.
As long as any one of source port/ip dest port/ip is differnent then it is a new flow and may be balanced accordingly.