Birkat ha’ilanot on trees grafted in a forbidden manner

Answer

1. Not all trees are grafted. Generally fig trees, pomegranate trees, and date palms are not grafted. While it is true that most trees are grafted, among those that are, most are grafted with the same species (min bemino), and this is permitted. Examples of trees that are grafted in a permissible way include: grapevines, olive trees, carob trees, and mango trees (among others).

An example of a tree that is almost certainly grafted in a prohibited fashion is the pear tree; 90% of pear trees in Israel today (2018) are grafted onto quince rootstocks. There are some fruit trees that are sometimes grafted onto forbidden rootstocks, such as plums, peaches (including nectarines), and apricots. Citrus fruit is grafted onto the same species or onto rootstocks that are safek mino (where it is uncertain whether it is the same species).  

2. There is a dispute among the poskim whether one should say birkat ha’ilanot (and shehechiyanu) on fruits and trees grafted in a prohibited fashion, and it seems that in practice one should not make this blessing on such fruit/fruit trees, since safek berachot lehakel (we are lenient when there is a doubt regarding blessings; see Kaf HaChayim OC §226:11 and §225:26).
3. Optimally, one should choose trees that are not generally grafted or that are grafted onto the same species. However, if you do not know whether the tree was grafted in a prohibited fashion, or for citrus trees—where in the worst case scenario the tree is grafted onto a tree that is safek mino—it seems that one can say birkat ha’ilanot.