Both V1 and V2 have unlimited version history by default. Each new file version is counted as a new file. Many customers have been using V1 backup for longer time period and version history has been building up all this time, whereas version history in V2 has only started to build.
Both V1 and V2 also have unlimited storing for deleted files/items. This means that V1 backup includes files and emails that have been backed up but later deleted from Microsoft 365. They will remain in V1 backup indefinitely - unless you have created retention policies to clear the oldest items, or manually deleted them from backup. None of these previously deleted items are present in V2 backup since all data has been backed up to V2 from scratch.
Considering the above, it is expected that item count and storage size in V2 backup is a bit lower than in V1.
However, if you notice anything missing from V2 backup, let our Support know exact details of the missing folders/items.