I am afraid I only have partial answers for you.

You mention that you work in a commercial environment. But that does not necessarily mean you need to use commercial tools or pathways, or does it?

If I read your question correctly you are not really asking about pathway tools, you are mainly asking about the pathway content used with the tools. Now commercial providers tend to offer one with the other, but that is not a necessity. You can often create or import your own pathways. Our own tool, PathVisio, for instance, can work with WikiPathways pathways as well as other pathways converted to the same format (Reactome, KEGG) or any other available in BioPAX format. Commercial tools also often allow addition of your own pathway collection.

That of course doesn't help you too much, since now your question will probably be whether bacterial pathways are available at all. I checked and we only have a few of those on WikiPathways. You can of course create more, but that might be more of a task that than you want to take up. You might consider it if you are working on a specific species. The worm and tuberculosis communities for instance are doing a fantastic job on that.

The metacyc project is really interesting for creation of species specific pathways. You might want to check whether a cyc for your specific species already exists, or if not create one. We have done some work in the past on automatic conversion of plant pathways from metacyc (tomato and arabidopsis) to WikiPathways format, but that is going slowly mainly because of lack of funding. It is doable however. So if this is important to you you might want to first create the cyc pathways and then work on the conversion.

You also ask about interacting compounds. These will usually not be in pathways at all, except for endogenous metabolites, and indeed drugs now and then. So what you will usually want to do is use an external resource to connect interacting compounds to (proteins in) pathways that are already there. There are several ways to do that, for instance using the Open PHACTS API to get compound-protein interactions (which will usually come from ChEMBL in that case). But that might go beyond your question.

It might seem off the wall to suggest experimentation as an answer but if (a big if I know) the bugs your interested are culturable comparative metabolic profiling is a more direct option. Unfortunately new metabolilte/enzyme pairings are few on the ground (as came up in this post). I cant quite work out the commercial angle on your 100 "chemistry suspects" but what you could do in silico is explore their similarity neighbourhood in PubChem in some detail. If your lucky you might connect to metabolic clues or even a natural product paper that links you to an organism. Note also that the metagenomic databases are stuffed with new strange enzyme sequences that will keep pathway annotators and experimental enzymologists (and structural biologists) busy for years.

EcoCyc is something that you should look into. It's focus is E. coli, but can be useful for other bacterial species. A partner database is BioCyc, a collection of 3563 Pathway/Genome Databases (PGDBs), with tools for understanding their data.