Do you have a picture of your tree? If the angle of the crotch where your branches are bifurcated is very accute, you may want to completely remove it.
Generally with Mangos grown in SoCal, I will now tell people not to mess with it much because the vegetative growth is so slow. Removing branches from a small tree growing this marginal climate where we get significantly fewer heat units than Asia and Southern Florida can stunt the tree. In some cases however, if the branches aren’t significant, it may be easier to remove when it’s younger so the tree can focus its energy on the Branch you’re going to keep.
Your Mallika and NDM will be good for taking scions from. If you can find it, try to get a hold of some NDM seeds. Maybe post a thread on the buy/sell forum when Mangos are ripening in Florida. NDM is Polyembryonic and I’ve found them to be excellent growers in SoCal. Sweet Tart and CAC are two other great tasting and excellent growers in SoCal that are also Polyembryonic.
When you plant these Polyembryonic seeds and if you’re lucky enough to get multiple sprouts from a seed with individual root systems, there is a good chance that at least one of the seedlings is a clone if you grow out at least two of the seedlings.
The benefit of growing trees from these Polyembryonic seeds is that you will not need to graft them if you are lucky enough to get a clone. Because the tree will not require grafting, it will continue to grow vegetatively until it reaches sexual maturity, however long that may be. In SoCal, you often don’t have to wait any longer than about 3-6 years.
I don’t believe I have ever mentioned this before but trees that are Not grafted at a young age( in SoCal) tend to have much better structural form because small grafted trees will often flower precociously causing a droopy structure.
If you plant a seedling and let it grow for several years, this will allow the scaffold branches to form and once you get the basic structure of the tree formed, you can begin to top work the scaffold branches.
Planting Polyembryonic seeds can help to avoid many of these issues but then Polyembryonic seeds have issues of their own that needs to be addressed.
Acquiring the seeds can be difficult and when planted, some will only have a single sprout so you won’t know if it’s a clone or the zygotic seedling. If you do get multiple sprouts with individual root systems, you still won’t know definitively which seedling/s are the clone so your best bet is to separate them and plant them both, or all ten!
I used to recommend that you just plant the seeds as is and keep two of the seedlings but I have since changed my thinking on this matter because as the two trees grow, they tend to push each other apart if not separated. Although this works, it may not give the grower the most structurally sound tree.
Simon