SQLite - Should I add some indexes even if select queries are fast?
Now, tables have max 5k rows and in future they may go maximum up to 100k rows


In cases like this, where time and resource permits, the best way to check this is to manufacture realistic looking data of that size and test your application against that to see how well it scales (or if it doesn't, where the bottlenecks lie). Make sure your data is realistic though: ~100,000 identical rows won't be a good test as the indexes will not be selective enough to be useful, likewise truly random numbers in the column where the data is expected to "bunch" would also not be the most useful test.