in fact, magmi uses the magento reindexer (the exact one that canbe called through ssh command line)
however, magmi also provides on the fly reindexer which can take care of :
- catalog_url_rewrite (one of the most demanding in terms of requests)
- catalog category product
so, you could uncheck those from magmi magento reindexer config (but keeping other indexes you need) & use the on the fly reindexer plugin.
this may save most of the processing needed.
If you only update products prices & stock (not creating new ones nor updating other attributes), you can just check price reindexing & inventory stock reindexing, which take much less time.