MySQL's "slow query" log: strange "Query_time"
Ah, I should have checked that first:

log_queries_not_using_indexes has been turned on, so a whole number of queries has been logged because they were not using indexes. 

Apparently, a query "not using indexes" is not marked in any way in the slow query log, so one has to guess whether an entry has been logged because of an execution time exceeding the long_query_time threshold or because of indexes.