No, it means the query has no data.  You need to talk to the person who wrote it.

But we had the same problem a few times already. We didn't make any changes to the code. While we were still investigating what is going on,  then after a couple hours, the query returns result. 

Talk to the person who wrote the app, this isn't a Sage problem.  It sounds like a poorly designed query timing out.

But it doesn't look like a timeout error. it simply returns empty bracket. It is not that the query running for a while and returns error. 

Talk to your programmer, this is not a Sage problem.

The only reason I could imagine data suddenly showing up in a query is that a Day End Processing (Inventory Control / Periodic Processing) hadn't been processed for the O/E, P/O or I/C transactions being queried - or that resulting A/R or A/P batches hadn't been posted yet.