If mobs are aggroing through walls, it could be a couple of issues. Most likely the issue is that you forgot to setup your /server/maps/ folder and add all of the .map folders from the repository. If you do that, there will be nothing on the server to block LoS. You can test this from a GM account by targetting an NPC and using the #los command. If they have LoS to you even when they definitely should not be able to see you, it is most likely due to missing map files.
Another thing it could be is a poorly made map file. Not all map files include all of the structures on that map such as houses/huts/trees/etc. and that means mobs can see through them. As long as there is a working map file, they still shouldn't be able to see through landscape such as hills though. If you need a better map file that includes more than just the basic stuff, you can create them using Azone2. It isn't very hard to create them once you know how, but I am not going to write a step-by-step process in this response.
The last possibility is that mobs are chain aggroing. Even if you can't see a mob, you can still aggro them in certain cases by chain/shared aggro. An example is if you pull a single mob that you can see, but that mob is also near another mob that it can see (but you can't), so it shares aggro with it. Then, that other mob may have LoS (line of sight) to yet another mob and so on. As long as they are within the range to share aggro, chain aggroing can get quite a bit more mobs than you would expect and they can definitely appear to be aggroing through walls.
The final issue you mentioned is NPCs actually running through walls to get to you. This isn't an issue with aggro, it is an issue with pathing. Creating pathing that prevents NPCs from running through walls isn't something that can be easily automated unfortunately. You do have an option, however, to create .path files that NPCs will use to make their pathing look much more live-like. There are not .path files for every zone in the repository, as it requires manual work for each zone to have a .path file created for the zone. You can find some examples in the repository such as PoKnowledge's .path file. A cool test for it is to zone to poknowledge and use #aggrozone (probably want to use #invul first). Then, watch as every NPC paths nicely without warping through walls. You can also use #hide on after to clear your aggro and watch them all walk back to their spawn point using the correct pathing to get there.
If you want to create .path files, I believe there is a post on how to do so in our development section from when that functionality was added.
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