You could export to ePUB from Indesign first and tweak your CSS file using an adjacent selector to put space before or after a paragraph when it is preceded by another paragraph. For example;
Code:
p + p {
margin-bottom:3em;
}
or
Code:
p.your-para-class + p.another-para-class {
margin-bottom:3em;
}
Then convert your ePUB to Mobi using Kindlegen (or Kindle Previewer). In the resulting mobi the space between the paras will be preserved.