First Bombs are considered Supernatural meaning yes they are magical, but they are not spells or spell-like. They cannot be dispelled and not subject to counterspells (this will be important later).

Detect Spells function by Caster Level and against a spell.

Bombs are not spells and they may duplicate spell effects but in the end they are still classified as Supernatural which still puts them in the, "not a spell category." If they duplicated the acutal spell then it'd be a Spell-Like Ability if anything. So when considering Detect Evil or Detect Magic, there is no category for Supernatural Effects.

One of the core differences between Spell-Like Abilties and Supernatural is what affects them. SLA are effected by Dispel Magic, Counter Magic, and Spell Resistance...all effects where there is a caster level check of some sort. Supernatural abilities are not which gives credence that they do not function on a caster level system. So again in short, Supernatural abilities do not have a caster level (this has been a long standing problem with them for the reason of detect spells).

So regardless right from the start there is an inherent problem with your Cleric, Paladin, or any Detect Evil bot trying to see the issue...it won't show up on their radar. Another paradoxical situation, Smoke Bomb Discovery...ask them how'd they resolve a Detect Magic strength on it?

What will show up is that your victims of said bombs will have these nasty diseases going so in the end though they may not be able to metagame a quick answer (the bomb is EVIL!)...they are going to notice your biological warfare overtime which innately does cater to being evil in most societies.

If the Cleric literally used the words, "Murder you," then I'd let it go for the enjoyment of seeing that alignment slide when they commit the deed and possibly see an interesting Paladin fall-from-grace moment. Most Lawful lands have some sort of court system and way of dispensing justice, and unless they were given the right of Judge/Jury/Executioner then it'd be at least the Paladins responsibility to see you are help to the law. Now when they come to detain you, if you put up any sort of resistance then most likely they can get away with removing your head.