Why don't stealth aircraft designs use podded engines?
Yes. From the PoV of stealth aircraft, the podded engine has significant disadvantages:


The engine pod has a high Radar Cross Section; In fact, stealth aircraft bury the engine inside their fuselages to minimize radar cross section. For example, the B2 Spirit engines were located inside the fuselage, as shown in the schematic below.





The exposed compressor blades in the podded engine reflects radar waves, which is not good. For example, in Boeing X-32, the location of the engine meant that the compressor blades will be exposed to the Radar and baffles were (proposed to be) added to reduce the Radar cross section. On the other hand, it can be seen that it is practically impossible to see the F-22 compressor blades from any angle of the inlet.




Source: f-16.net


In case of podded engine, it is difficult to shield the exhaust thermal signature. Compare the infrared signature of the typical airliner in the following picture with that of the B-2 Spirit in the next picture.




Source: laserfocusworld.com



Source: bestfighter4canada.blogspot.in

Of course, contemporary combat aircraft don't use podded engines at all (with the exception of the A-10, which is a ground attack aircraft).