Frankly I'm not a huge fan of the idea of bringing D&D-style cleric spells into IVAN. While they're not something commonly seen in roguelikes, they definitely are in found in other RPGs. If magic is implemented in IVAN, it shouldn't follow any established system IMO.
Simply increasing object weight would not really hamper the power hoarding, as you're not required to carry the items with you everywhere. Stashing things in a chest on the previous stairs (level above or otherwise) already gives a nigh-foolproof way of keeping your things safe from hungry bunnies, explosions and the like. You'd simply keep a smaller portion of your supplies with you, which hardly ever actually becomes a problem.
I do like the idea of dropping the amount of trades per prayer, but even that fails to properly address the problem given another good source of food like polypiling or Seges. You'd still be capable of amassing a pile of healing and ommel substances with time. In addition, making the better items too rare could highly detract from his actual feel of usefulness especially for newer players. Simply put, trading empty bottles for ones full of water or poison isn't exciting.
To be frank, right now Mellis does not really match the description of being a god of trade. Filling an empty container hardly counts for trading. While walking to work this morning, I came up with two solutions to both nerf him and giving him more of a trading aspect.
1) Instead of simply filling a container you have, trade it for a full container of a different kind. In addition to making the effect more like a trade, this would also slow down the process of stockpiling power by not letting you simply keep using the same containers over and over again. You could also make this cyclical instead of random. Trading an empty bottle could give you a can of stuff, which could then be traded for a banana and further back into a bottle. With only the three containers currently in IVAN this doesn't make too much of a difference, but new containers could be added. Even more, by restricting certain substances to specific containers, the effect itself would become much more interesting by allowing you to trade items for a specific subset of results.
This should probably be combined with a lower amount of trades per prayer as well to slow down the cycling and to keep the effect power down.
2) A more radical approach would be to abandon the current effect of getting full containers completely. Instead, let Mellis trade your items for prayer effects of different gods based on the alignment and value of the traded item. For example, standing on an iron dagger and praying to Mellis could consume the dagger and give you haste if you're at favourable standing with Cleptia. Offering a very valuable item could even let you gain the effects of gods who currently hate you, like trading an arcanite staff of wondrous smells +6 for Infuscor's ESP effect at Lawful++. This again would be much more interesting of an effect than the current container filling. The prayer should still only affect your standing with Mellis to prevent essentially getting two prayer's worth of standing combined with a normal prayer every 3 hours for the god in question.
These two effects wouldn't even necessarily need to be mutually exclusive.
Simply put, dexterity and agility are lowered if the equipment you're wearing is not flexible enough for your current score. The penalty varies by material, equipment type, equipment slot and your current stats. Troll hide for instance is very stiff, which limits your movement especially when used for things like cloaks. The two other ways the gray number appears is either by using equipment that boosts your stats, or by sustaining debilitating injuries (greyed out) to a limb or your head.