You have hot temps, that's cute. Try hard incline's going up and down passes. Makes "hot dry temps" seem laughable.
But please, tell all you know about how the engine was designed, tested, and how your fluid dynamics calculations and simulations have worked out.
Sorry, but there are few hood vents out there that are worth a sh*t.
And yeah, I've known plenty of AZ and SoCal folk (lived in SoCal for a brief stint myself) with lifted rigs that don't have issues.
So tell me, the engine should have no problem seeing water on top of it? Now, how does what work when they came from the factory with wheel well liners, a hood, and more to prevent water intrusion? Last time I checked, none of the electrical fittings were water proof. Want to guess how I unfortunately know?
The heatsoak with the precat system can largely be solved with the heat shield that should still be next to the intake manifold and surrounding the injectors (I own a 2001, and know several that do).
But no, by all means, throw holes in your hood...hell take the hood right off!
Those OEM calculations were with all the splashguards in place, stock tires, etc, etc, etc. In stop and go traffic and yes, some mild offroad. Keep in mind the Cherokee was designed as a ski chalet or "I don't want to drive an Impreza" type vehicle, not a rock crawler. OEM engineers make lots of decisions that involve more than just keeping it cool under all conditions: emissions, cost, packaging, ease of production/servicing (which they didn't do a very good job of

), etc. Compromises were made.
When I first started wheeling my XJ, my 100% new, flushed and stock cooling system kept up fine with offroading, but my trans cooler and power steering fluid were not at all appreciative. In goes the auxiliary coolers for these items in the only place they would be effective: in front of the radiator. The stock cooling system was no longer happy, so I added a ZJ fan clutch. My temps still creep a little (220* on hot wheeling trips), but at least it's no longer boiling over.
That being said, popping the hood on a hot day requires gloves or a dangerous game of hot potato with the hood prop and the hood due to the crazy high underhood temps, and can't be good for the electronics. Every piece of wire loom, electrical tape, connector and any other piece of plastic is brittle as can be from the heat soak, so I don't think leaving the heat in there is a good thing either.
As for the harness not being weather tight: every connector I've seen under the hood has weather seals on both the connector side and the wire side. I'm sure the weather seals have seen better days (probably from the heatsoaking), so I help them out with dielectric grease and have replaced some of the loom and electrical tape that since cracked off (pretty much everything on top of the intake manifold from the exhaust heat). Keep in mind that all of the connectors on the bottom side of the engine bay (O2 sensors, transmission sensors/connectors, fuel tank related connectors) are all constantly exposed to direct water spray and are reliable as can be expected. These connectors use the same sealing system that the ones on the top of the engine use.
So, why not install an electric fan bypass?
How about a better than OEM pump?
How old is you radiator?
When's the last time you stripped the system down and did a full block flush?
If you're not overheating, then why the **** are you concerned?
It's an engine...it gets hot.
Again: my 100% refreshed cooling system worked fine in SoCal deserts/mountains, but the other hydraulic systems did not. Adding coolers for these items overtaxed the stock coolant system.
Yes, it's an engine. Yes, it gets hot. This is, by far, the hottest under hood engine I've been exposed to, and that includes turbo time attack cars making 5x the power from half the displacement with airflow optimized entirely for downforce, not cooling (more air to the coolers means less downforce). I've never needed gloves just to open the hood on those vehicles.
In any case, I think the heat is worse for these 20-ish year old vehicles than occasional water, especially when you consider that most of the places where it's often 100*+ with low humidity (worst case for cooling since hot/dry air has less heat propensity) don't see rain very often.