The nacelle is not some solid block. For the flow it looks like a hollow, slightly blocked tube.
The flow ahead of the nacelle is indeed slowed down in flight, but only a little, entering the intake face at a flow speed of around Mach 0.4 to 0.5. This compresses the air ahead of the nacelle when flying in cruise at around Mach 0.8, so what enters the intake is already slightly compressed. Note that this compression does not involve boundary layers or shocks, so it is very efficient. The effect of the compression is that some of the air flowing towards the nacelle is pressed aside to flow around it. To avoid flow separation, the intake lip is rounded.
Pre-compression helps, because it raises the pressure in the whole engine and increases its thrust. What might be looked at as drag is in fact increasing the thrust of the engine! Of course, by further compressing and heating the ingested air the engine accelerates it, so the outflow speed of the core flow is easily double its entry speed. The outflow fills up the cross section of the engine, so the outer flow never has to flow into a void and experience separation (which is responsible for most of the drag of blunt bodies). Instead, it meets a faster jet of air once it has passed the engine fairing and is accelerated during the mixing process.
Only if the engine is idling or off will the nacelle cause real drag.