Keep in mind that I don’t use Intaglio. I’ll just answer in general terms.
The typical way to handle this kind of problem would be with styles. Instead of coloring a certain element blue, you would create a blue-fill style and apply that to all of the elements you want to be blue, and then later you can change the color of the blue-fill style to red and all the blue elements change color to red.
It looks like Intaglio does support AppleScript. If you are creating complicated vector documents or multiple vector documents, you probably owe it to yourself to learn to script your editor. Otherwise you will spend a ton of wasted time laboriously going through element after element, making the same change, dulling your mind. That is why AppleScript exists in the first place, so that you can work 100% creatively, and AppleScripts do the grunt work. Learning to script your first app is a bit daunting, but very rewarding. You can also script TextWrangler with AppleScript, so you can create AppleScripts that automate TextWrangler and Intaglio as if they were one app that can create almost any website.
What you are describing with a text search-replace would work with SVG because they are just XML documents made of plain UTF-8 text. It is unlikely that your native Intaglio document is stored as plain text. You could point TextWrangler to a folder full of SVG and replace #99FFFF with #FFCCCC. Keep in mind that the colors in an SVG could also be written as rgb(153, 255, 255) or or rgba(153, 255, 255, 0) — with or without spaces. But round-tripping from your editor’s native vector document format to SVG and back again could mean a loss of fidelity because SVG may not support all of the features of an Intaglio document, or Intaglio’s SVG export and import may not support all the features of SVG. But if you are making SVG anyway, you can export as SVG and just work as you would with any other Web document. That is a key feature of SVG.