Studies have shown that when bio-identical estrogen is taken non-orally, clotting is much less affected. In men with prostate cancer, for example, given high doses of estradiol transdermally (patches) or parenterally (injections), it was concluded by the authors that cardiovascular incidence and thrombosis was not increased and that transdermal estradiol was actually protective. But, the risk of clotting does increase somewhat in pregnant women whose levels of estrogen sharply rise, more so in women predisposed to it. There are also other factors that could contribute to clotting and during pregnancy, there are so many other things going on so who knows?
Bio-identical estradiol also appears to affect clotting much less than other estrogens like Premarin or ethinyl estradiol contained in birth control pills.
Based on all that evidence so far, it would seem that taking bio-identical estradiol, especially non-orally would cut down the risks significantly but as always, we all react differently. Some could be more prone to DVT than other based on a whole array of factors that your doctor needs to determine.
If you feel any of the symptoms of DVT coming on which you should ask your doctor what those symptoms are or check the internet, it's important to immediately contact health services/emergency, etc.
Also, one must realize that other medications can also affect clotting such as cyproterone acetate, medroxyprogesterone acetate, etc.