Minecraft – limit the amount of mobs within a chunk

As of the Minecraft version at the time of writing this...

Tamed wolves are not a passive mob and they do not have any limit, so they will not affect the passive mob limit (because if they were counted in the passive mob limit there would be a limit on the number you can tame.)

Passive mobs (a pig, for example) will NEVER attack you, even if you attack them.

Wolves are actually tame, meaning they follow and protect you.

Short answer:

Tamed wolves do NOT affect the passive mob limit in any way.

No, there's no limit to how many items can be in a chunk, nor in a pipe. I've piped a rotary macerator at full speed into a cobblestone pipe, and it handles them fine. The limitations of pipes are designed entirely around transport speed, not contents capacity. Minecraft's limitations on items aren't designed into the game mechanics — rather, too many items will simply overload memory and slow your server to a crawl.

Since you have a long pipeline, you are likely having parts of it unload when there are no players around that section. When this happens, the items can drop out of the last section of loaded pipes since they aren't "connected" to anything. You're probably seeing this more with all the quarries running simply because more items mean more chances to have part of a pipe that should be receiving items be unloaded at any given time. The easiest way to get around this is to make sure the chunks that have pipes running through them are always loaded by using World Anchors, Anchor Carts, or another block that designates a chunk to stay loaded even with no players around.

(As an alternative to buildcraft pipes you could also use RedPower2 pneumatic tubes. These won't transport items through unloaded chunks, but they have a more favourable failure mode: when a pipe can't deliver, items just rebound and get "backed up" in the tubes until there's somewhere for them to go. This would lower your throughput compared to a proper Anchor solution though, and would require rebuilding your item transport system over the entire long distance.)