Please check configuration of SCOM Agent co-located with Veeam collector (see KB1026)
, make sure you don't have "Veeam Collector: Health Service dropped data" or "Veeam Collector: Health Service workflows failed" alerts raised (KB1765
If no additional alerts indicating performance issues with SCOM Agent occur, you can try increasing thresholds for 2 monitors based on current number of handles:
1) MonitoringHosts.exe "Veeam Collector: Health Service (Monitoring Host) Handle Count threshold"
2) HealthService.exe "Veeam Collector: Health Service Handle Count threshold"
Otherwise you may consider moving VMware monitoring jobs to other Veeam Collectors or co-locating Veeam Collector with a SCOM Management Server.