The most time consuming part would be editing the ini files, etc. I basically did this a while back, in a fashion, for vanilla Freelancer, it took a few days of grinding, but nothing insurmountable. The ships aren't a problem, just take a few minutes to set the stats of the originals to the Mk.IIs. It's only a few paragraphs of text in the ini files, so it doesn't appreciably affect performance or size just to leave them.
Weapons themselves are the nuisance, because of the sheer NUMBER of them, and the references throughout the game to the COUNTLESS variants of them. Headache, big time.
With the Mk.II ships, this is in essence only affecting VERY new players as far as their ships and equipment are concerned. If you've been playing a few hours, you're long gone from starting grade ships anyway. I had a decent fit centurion by the end of the first day and a little scratch on the side. From this standpoint it's not worth bothering with. Make Mk.II versions of the one or two ships that don't already have them. If you're concerned about starting drag (which it is GRUELING AND HORRIBLE to start in freelancer) then up the starting cash a bit. 50k, 100k? Enough to get a decent starter ship.
The only thing this affects to a SERIOUS degree is the NPCs. Currently, passing Mk.II patrols and capships mean you can't go AFK in Liberty (if you're unlawful anyway) but for the most part, once you leave lib, they're no longer a threat to you. It would even this out and encourage people to depart liberty and spread out. This is annoying, but not THAT big of a deal.
Contrary to popular belief, NPCs don't interfere THAT much. I watch corsairs RP all the time in Omicron. You can't completely ignore them while they wail ineffectually on your ship, but it's not that bad. If you need/want to type pages and pages of text, dock or use the forum. Or head a couple k above the horizontal plane till NPCs quit spawning (this). I don't know if many people are aware or think of that last one, but I swear to god it works. That's the ideal for in-game RP.
Now what IS cool about trimming down the number of weapons and equipment is it gives the devs more room to work with on their end, so they can specialize things a little more. And I like the idea of Liberty ships being unable to mount other weapons, etc. Instead of class being a power scale thing, it's just a way to specify certain equipment being used. This is the primary plus to doing this in my opinion.