Core component of SQL Server for storing, processing, and securing data
The short answer is: It depends.
I realise that this is not the answer you want to hear, but there are rarely short simple answers to situations like this. Typically, you have to dig into one query at a time to see how it can be improved by better indexing. Since you are loading lots of data, breaking up the operations in chunks can also help, if done in the right way.
As for your question: Keep in mind that rebuilding an index updates the statistics the index as well, and with fullscan. That is, you get statistics that are based on all the data rather than just a sample. So this is a bad thing to do:
ALTER INDEX ALL ON tbl REBUILD
UPDATE STATISTICS tbl
The second statement will replace fullscan statistics with sampled statistics which are less accurate. (But in many cases, they are still perfectly satisfactory.)
Rebuilding all indexes on 35000 tables may take more time than you have to for the operation. One thing to keep in mind that fragmentation in the sense that pages do not come in order on the disk matters a lot less today with SSDs than what it did in the days of spinning disk. But another thing is how much data there is on every page. If every page is half-full, this means that you 50% of your buffer cache contains - vacuum. I don't which sort of fragmentation you are talking about, but I suspect that it is the former, because that is easier to compute for SQL Server.