"Scattered" means widely distributed, not in groups but individually. So it means that there are many truths to be found at intervals throughout the Bible.

The point of the simile of "pearls" here is value. "Pearls of wisdom" is a very long-established idiomatic expression, still commonly used. Pearls are rare, valuable, beautiful and brilliant white, almost luminous: qualities appropriate to the spiritual wisdom found in the Bible.

"As so many pearls" literally means "like the same number of pearls"; in other words, every one of these biblical truths is like a pearl.

The author (Thomas Watson) is probably thinking here of a quotation from the Bible, from the Sermon on the Mount (Matthew 7:6), which is expressed in the early-seventeenth-century King James version as: "Give not that which is holy unto the dogs, neither cast ye your pearls before swine, lest they trample them under their feet, and turn again and rend you". This brings the implication that biblical truths are only correctly understood by those worthy and capable of receiving them.