Are there economic models that predict (only) a medium/long-term negative effect of protectionism?
This is not exactly what I was looking for, but seems "good enough":

I found a recent empirical paper by IMF staff (Furceri et al., 2018) applying Jorda’s local projection method to a panel of data of 151 countries over 1963-2014. They found/predict negative effects from the first year after the measures are introduced, but the effect size on output looks pretty small and given the confidence band it can well still go up for some years after the measures are introduced.



They also have bunch robustness checks (alternative models) which mostly preserve/confirm that conclusion



The "drop early years (&lt;1980)" seems to produce a different enough result on output though (in that robustness graph), but I can't find any commentary on that particular check in the paper. I guess it's because it still falls within the 90% confidence region of the base model. The paper does point out in its introduction that older data had more protectionism:


  Our panel of annual data is long if unbalanced,
  covering 1963 through 2014; more recent data is of greater relevance, but older data
  contains more protectionism. Since little protectionism remains in rich countries, we use a
  broad span of 151 countries, including 34 advanced and 117 developing countries.




As an US addendum, regarding the Trump economy in particular, Kenny LJ answered another (much broader) question by citing/meniotining Fajgelbaum et al. (March, 2019)


  We analyze the impacts of the 2018 trade war on the U.S. economy. We estimate import demand and export supply elasticities using changes in U.S. and retaliatory tariffs over time. Imports from targeted countries declined 31.5% within products, while targeted U.S. exports fell 11.0%. We find complete pass-through of U.S. tariffs to variety-level import prices. Using a general equilibrium framework that matches these elasticities, we compute the aggregate and regional impacts. Annual consumer and producer losses from higher costs of imports were \$68.8 billion (0.37% of GDP). After accounting for higher tariff revenue and gains to domestic producers from higher prices, the aggregate welfare loss was \$7.8 billion (0.04% of GDP). U.S. tariffs favored sectors located in politically competitive counties, but retaliatory tariffs offset the benefits to these counties. We find that tradeable-sector workers in heavily Republican counties were the most negatively affected by the trade war.


So noticeable effect on trade already, but very small on GDP, percentage-wise. Given the IMF/Fuceri model, we don't really expect a large impact on GDP anyway.